Full wwPDB EM Validation Report i - PDBj top page

Full wwPDB EM Validation Report i○

Dec 13, 2020 – 06:37 AM EST

PDB ID : 6CRZEMDB ID : EMD-7577

Title : SARS Spike Glycoprotein, Trypsin-cleaved, Stabilized variant, C3 symmetryAuthors : Kirchdoerfer, R.N.; Wang, N.; Pallesen, J.; Turner, H.L.; Cottrell, C.A.;

McLellan, J.S.; Ward, A.B.Deposited on : 2018-03-19

Resolution : 3.30 Å(reported)Based on initial models : 5I08, 5X4S, 2AJF

This is a Full wwPDB EM Validation Report for a publicly released PDB entry.

We welcome your comments at [email protected] user guide is available at

https://www.wwpdb.org/validation/2017/EMValidationReportHelpwith specific help available everywhere you see the i○ symbol.

The following versions of software and data (see references i○) were used in the production of this report:

EMDB validation analysis : 0.0.0.dev61Mogul : 1.8.5 (274361), CSD as541be (2020)

MolProbity : 4.02b-467Percentile statistics : 20191225.v01 (using entries in the PDB archive December 25th 2019)

Ideal geometry (proteins) : Engh & Huber (2001)Ideal geometry (DNA, RNA) : Parkinson et al. (1996)

Validation Pipeline (wwPDB-VP) : 2.15.1

https://www.wwpdb.org/validation/2017/EMValidationReportHelp



https://www.wwpdb.org/validation/2017/EMValidationReportHelp#references

Full wwPDB EM Validation Report EMD-7577, 6CRZ

1 Overall quality at a glance i○

The following experimental techniques were used to determine the structure:ELECTRON MICROSCOPY

The reported resolution of this entry is 3.30 Å.

Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown inthe following graphic. The table shows the number of entries on which the scores are based.

Metric Whole archive(#Entries)

EM structures(#Entries)

Clashscore 158937 4297Ramachandran outliers 154571 4023

Sidechain outliers 154315 3826

The table below summarises the geometric issues observed across the polymeric chains and their fitto the map. The red, orange, yellow and green segments of the bar indicate the fraction of residuesthat contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria respectively. A greysegment represents the fraction of residues that are not modelled. The numeric value for eachfraction is indicated below the corresponding segment, with a dot representing fractions <=5%The upper red bar (where present) indicates the fraction of residues that have poor fit to the EMmap (all-atom inclusion < 40%). The numeric value is given above the bar.

Mol Chain Length Quality of chain

1 A 1215

1 B 1215

1 C 1215

2 D 3

2 F 3

2 J 3

2 K 3

2 M 3Continued on next page...

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#overall_quality


Continued from previous page...Mol Chain Length Quality of chain

2 N 3

2 R 3

2 T 3

2 U 3

3 E 4

4 G 2

4 H 2

4 I 2

4 L 2

4 O 2

4 P 2

4 Q 2

4 V 2

5 S 4


2 Entry composition i○

There are 6 unique types of molecules in this entry. The entry contains 25909 atoms, of which 0are hydrogens and 0 are deuteriums.

In the tables below, the AltConf column contains the number of residues with at least one atomin alternate conformation and the Trace column contains the number of residues modelled with atmost 2 atoms.

• Molecule 1 is a protein called Spike glycoprotein,Fibritin.

Mol Chain Residues Atoms AltConf Trace

1 A 1068 Total C N O S8339 5328 1379 1586 46 0 0

1 B 1068 Total C N O S8342 5331 1379 1586 46 0 0

1 C 1069 Total C N O S8343 5329 1380 1588 46 0 0

There are 42 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceA 577 ALA SER conflict UNP P59594A 968 PRO LYS engineered mutation UNP P59594A 969 PRO VAL engineered mutation UNP P59594A 1191 GLY - linker UNP P59594A 1192 SER ALA linker UNP D9IEJ2A 1220 GLY - expression tag UNP D9IEJ2A 1221 ARG - expression tag UNP D9IEJ2A 1222 SER - expression tag UNP D9IEJ2A 1223 LEU - expression tag UNP D9IEJ2A 1224 GLU - expression tag UNP D9IEJ2A 1225 VAL - expression tag UNP D9IEJ2A 1226 LEU - expression tag UNP D9IEJ2A 1227 PHE - expression tag UNP D9IEJ2A 1228 GLN - expression tag UNP D9IEJ2B 577 ALA SER conflict UNP P59594B 968 PRO LYS engineered mutation UNP P59594B 969 PRO VAL engineered mutation UNP P59594B 1191 GLY - linker UNP P59594B 1192 SER ALA linker UNP D9IEJ2B 1220 GLY - expression tag UNP D9IEJ2B 1221 ARG - expression tag UNP D9IEJ2B 1222 SER - expression tag UNP D9IEJ2B 1223 LEU - expression tag UNP D9IEJ2B 1224 GLU - expression tag UNP D9IEJ2

Continued on next page...

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#entry_composition


Continued from previous page...Chain Residue Modelled Actual Comment Reference

B 1225 VAL - expression tag UNP D9IEJ2B 1226 LEU - expression tag UNP D9IEJ2B 1227 PHE - expression tag UNP D9IEJ2B 1228 GLN - expression tag UNP D9IEJ2C 577 ALA SER conflict UNP P59594C 968 PRO LYS engineered mutation UNP P59594C 969 PRO VAL engineered mutation UNP P59594C 1191 GLY - linker UNP P59594C 1192 SER ALA linker UNP D9IEJ2C 1220 GLY - expression tag UNP D9IEJ2C 1221 ARG - expression tag UNP D9IEJ2C 1222 SER - expression tag UNP D9IEJ2C 1223 LEU - expression tag UNP D9IEJ2C 1224 GLU - expression tag UNP D9IEJ2C 1225 VAL - expression tag UNP D9IEJ2C 1226 LEU - expression tag UNP D9IEJ2C 1227 PHE - expression tag UNP D9IEJ2C 1228 GLN - expression tag UNP D9IEJ2

• Molecule 2 is an oligosaccharide called beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose.


2 D 3 Total C N O39 22 2 15 0 0

2 F 3 Total C N O39 22 2 15 0 0

2 J 3 Total C N O39 22 2 15 0 0

2 K 3 Total C N O39 22 2 15 0 0

2 M 3 Total C N O39 22 2 15 0 0

2 N 3 Total C N O39 22 2 15 0 0

2 R 3 Total C N O39 22 2 15 0 0



Continued from previous page...Mol Chain Residues Atoms AltConf Trace

2 T 3 Total C N O39 22 2 15 0 0

2 U 3 Total C N O39 22 2 15 0 0

• Molecule 3 is an oligosaccharide called alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose.


3 E 4 Total C N O50 28 2 20 0 0

• Molecule 4 is an oligosaccharide called 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose.


4 G 2 Total C N O28 16 2 10 0 0

4 H 2 Total C N O28 16 2 10 0 0

4 I 2 Total C N O28 16 2 10 0 0

4 L 2 Total C N O28 16 2 10 0 0

4 O 2 Total C N O28 16 2 10 0 0

4 P 2 Total C N O28 16 2 10 0 0

4 Q 2 Total C N O28 16 2 10 0 0

4 V 2 Total C N O28 16 2 10 0 0


• Molecule 5 is an oligosaccharide called alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose.


5 S 4 Total C N O50 28 2 20 0 0

• Molecule 6 is 2-acetamido-2-deoxy-beta-D-glucopyranose (three-letter code: NAG) (formula:C8H15NO6).

Mol Chain Residues Atoms AltConf

6 A 1 Total C N O56 32 4 20 0

6 A 1 Total C N O56 32 4 20 0

6 A 1 Total C N O56 32 4 20 0

6 A 1 Total C N O56 32 4 20 0

6 B 1 Total C N O70 40 5 25 0

6 B 1 Total C N O70 40 5 25 0



Continued from previous page...Mol Chain Residues Atoms AltConf

6 B 1 Total C N O70 40 5 25 0

6 B 1 Total C N O70 40 5 25 0

6 B 1 Total C N O70 40 5 25 0

6 C 1 Total C N O84 48 6 30 0

6 C 1 Total C N O84 48 6 30 0

6 C 1 Total C N O84 48 6 30 0

6 C 1 Total C N O84 48 6 30 0

6 C 1 Total C N O84 48 6 30 0

6 C 1 Total C N O84 48 6 30 0


3 Residue-property plots i○

These plots are drawn for all protein, RNA, DNA and oligosaccharide chains in the entry. Thefirst graphic for a chain summarises the proportions of the various outlier classes displayed in thesecond graphic. The second graphic shows the sequence view annotated by issues in geometry andatom inclusion in map density. Residues are color-coded according to the number of geometricquality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2and red = 3 or more. A red diamond above a residue indicates a poor fit to the EM map forthis residue (all-atom inclusion < 40%). Stretches of 2 or more consecutive residues without anyoutlier are shown as a green connector. Residues present in the sample, but not in the model, areshown in grey.

• Molecule 1: Spike glycoprotein,Fibritin

Chain A:

SER

ASP

LEU

ASP

R18�

C19�

T20�

T21�

F22�

D23�

D24�

V25�

Q26�

A27�

P28�

N29�

Y30�

T31�

Q32�

H33�

T34

S35�

S36�

M37�

R38�

G39�

V40

Y41�

Y42�

P43�

D44�

E45�

I46�

F47�

R48�

S49�

D50�

T51�

L52�

Y53�

L54�

T55�

Q56�

D57�

L58�

F59�

L60�

P61

F62�

Y63�

S64�

N65�

V66�

T67�

G68�

F69�

H70�

T71�

I72�

N73�

H74

�T7

5�

F76

�G7

7�

N78

�P7

9�

V80

�I8

1�

P82

�F8

3�

K84

�D8

5�

G86

�I8

7�

Y88

�F8

9�

A90

�A9

1�

T92

�E9

3�

K94

�S9

5�

N96

�V9

7�

V98

�R9

9�

G100

�W1

01�

V102

�F1

03�

G104

�S1

05�

T106

�M1

07�

N108

�N1

09�

K110

�S1

11�

Q112

�S1

13�

V114

�I1

15�

I116

�I1

17�

N118

�N1

19�

S120

�T1

21�

N122

�V1

23�

V124

�I1

25�

R126

�A1

27�

C128

�N1

29�

F130

�E1

31�

L132

�C1

33�

D134

�N1

35�

P136

�F1

37�

F138

�A1

39�

V140

�S1

41�

K142

�P1

43�

M144

�G1

45�

T146

�Q1

47�

T148

�H1

49�

T150

�M1

51�

I152

�F1

53�

D154

�N1

55�

A156

�F1

57�

N158

�C1

59�

T160

�F1

61�

E162

�Y1

63�

I164

�S1

65�

D166

�A1

67�

F168

�S1

69�

L170

�D1

71�

V172

�S1

73�

E174

�K1

75�

S176

�G1

77�

N178

�F1

79�

K180

�H1

81�

L182

�R1

83�

E184

�F1

85�

V186

�F1

87�

K188

�N1

89�

K190

�D1

91�

G192

�F1

93�

L194

�Y1

95�

V196

�Y1

97�

K198

�G1

99�

Y200

�Q2

01P2

02�

I203

�D2

04�

V205

�V2

06�

R207

�D2

08�

L209

�P2

10�

S211

�G2

12�

F213

�N2

14�

T215

�L2

16�

K217

P218

�I2

19�

F220

�K2

21�

L222

�P2

23�

L224

�G2

25�

I226

�N2

27�

I228

�T2

29�

N230

�F2

31�

R232

�A2

33I2

34�

L235

�T2

36�

A237

�F2

38�

S239

�P2

40�

ALA

GLN

ASP

I244

�W2

45�

G246

�T2

47�

S248

�A2

49�

A250

�A2

51�

Y252

�F2

53�

V254

�G2

55�

Y256

�L2

57�

K258

P259

�T2

60�

T261

�F2

62�

M263

�L2

64�

K265

�Y2

66�

D267

�E2

68�

N269

�G2

70�

T271

�I2

72�

T273

D274

�A2

75�

V276

�D2

77�

C278

�S2

79�

Q280

�N2

81�

P282

�L2

83�

A284

�E2

85�

L286

K287

�C2

88�

S289

�V2

90�

K291

�S2

92�

F293

�E2

94�

I295

�D2

96�

K297

G298

�I2

99�

Y300

�Q3

01�

T302

�S3

03�

N304

�F3

05�

R306

�V3

07�

V308

�P3

09�

S310

�G3

11�

D312

�V3

13�

V314

�R3

15�

F316

�P3

17�

N318

�I3

19�

T320

�N3

21�

L322

�C3

23�

P324

�F3

25�

G326

�E3

27�

V328

�F3

29�

N330

�A3

31�

T332

�K3

33�

F334

�P3

35�

S336

�V3

37�

Y338

�A3

39�

W340

�E3

41�

R342

�K3

43�

K344

�I3

45�

S346

�N3

47�

C348

�V3

49�

A350

�D3

51�

Y352

�S3

53�

V354

�L3

55�

Y356

�N3

57�

S358

�T3

59�

F360

�F3

61�

S362

�T3

63�

F364

�K3

65�

C366

�Y3

67�

GLY

VAL

SER

A371

�T3

72�

K373

�

L374

�N3

75�

D376

�L3

77�

C378

�F3

79�

S380

�N3

81�

V382

�Y3

83�

A384

�D3

85�

S386

�F3

87�

V388

�V3

89�

K390

�G3

91�

D392

�D3

93�

V394

�R3

95�

Q396

�I3

97�

A398

�P3

99�

G400

�Q4

01�

T402

�G4

03�

V404

�I4

05�

A406

�D4

07�

Y408

�N4

09�

Y410

�K4

11�

L412

�P4

13�

D414

�D4

15�

F416

�M4

17�

G418

�C4

19�

V420

�L4

21�

A422

�W4

23�

N424

�T4

25�

R426

�N4

27�

I428

�D4

29�

A430

�T4

31�

S432

�T4

33�

G434

�N4

35�

Y436

�N4

37�

Y438

�K4

39�

Y440

�R4

41�

Y442

�L4

43�

R444

�H4

45�

G446

�K4

47�

L448

�R4

49�

P450

�F4

51�

E452

�R4

53�

D454

�I4

55�

S456

�N4

57�

V458

�P4

59�

F460

�S4

61�

P462

�D4

63�

G464

�K4

65�

P466

�C4

67�

T468

�P4

69�

P470

�A4

71�

L472

�N4

73�

C474

�Y4

75�

W476

�P4

77�

L478

�N4

79�

D480

�Y4

81�

G482

�F4

83�

Y484

�T4

85�

T486

�T4

87�

G488

�I4

89�

G490

�Y4

91�

Q492

�P4

93�

Y494

�R4

95�

V496

�V4

97�

V498

�L4

99�

S500

�F5

01�

E502

�LE

ULE

UAS

NAL

APR

OAL

AT5

09�

V510

�C5

11�

G512

�P5

13�

K514

�L5

15�

S516

�T5

17�

D518

�L5

19�

I520

�K5

21�

N522

�Q5

23�

C524

�V5

25�

N526

�F5

27�

N528

�F5

29�

N530

�G5

31�

L532

�T5

33�

G534

�T5

35�

G536

�V5

37�

L538

�T5

39�

P540

�S5

41�

S542

K543

�R5

44�

F545

�Q5

46�

P547

�F5

48�

Q549

�Q5

50�

F551

�G5

52�

R553

�

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#residue_plots


D554

�V5

55�

S556

�D5

57�

F558

�T5

59�

D560

�S5

61�

V562

�R5

63�

D564

�P5

65�

K566

�T5

67S5

68�

E569

�I5

70�

L571

�D5

72�

I573

�S5

74�

P575

�C5

76�

A577

�F5

78�

G579

�G5

80�

V581

�S5

82�

V583

�I5

84T5

85�

P586

G587

T588

�N5

89�

A590

�S5

91�

S592

�E5

93�

V594

�A5

95�

V596

�L5

97�

Y598

�Q5

99�

D600

�V6

01�

N602

�C6

03�

T604

�D6

05�

V606

�

A609

�I6

10�

H611

�A6

12�

D613

�Q6

14�

L615

�T6

16�

P617

�A6

18�

W619

�R6

20�

I621

�Y6

22�

S623

�T6

24�

G625

N626

�N6

27�

V628

�F6

29�

Q630

�T6

31�

Q632

�A6

33�

G634

�C6

35�

L636

�I6

37�

G638

�A6

39�

E640

�H6

41�

V642

�D6

43�

T644

�S6

45�

Y646

�E6

47�

C648

�D6

49�

I650

�P6

51�

I652

�G6

53�

A654

�G6

55I6

56�

C657

�A6

58�

S659

�Y6

60�

H661

�T6

62�

VAL

SER

LEU

LEU

ARG

SER

THR

SER

GLN

K672

�S6

73�

I674

�

V675

A676

�Y6

77�

T678

�M6

79�

S680

�L6

81�

G682

�A6

83�

D684

�S6

85�

S686

I687

�A6

88Y6

89�

S690

�

T693

�I6

94A6

95�

I696

P697

�T6

98N6

99�

F700

�S7

01�

I702

�S7

03�

I704

�T7

05�

T706

�E7

07V7

08�

V711

S712

�M7

13�

A714

K715

�T7

16S7

17�

V718

D719

�C7

20�

N721

�M7

22�

Y723

I724

�C7

25�

G726

�D7

27�

S728

�T7

29�

E730

�C7

31A7

32�

N733

�L7

34�

L735

�L7

36�

Q737

�Y7

38�

G739

�S7

40�

F741

C742

�T7

43�

Q744

�L7

45N7

46�

R747

�A7

48L7

49�

S750

�

A753

�A7

54�

E755

Q756

�D7

57�

R758

�N7

59�

T760

�R7

61�

E762

V763

�F7

64�

A765

�Q7

66�

V767

�K7

68�

Q769

�M7

70�

Y771

�K7

72�

T773

�P7

74�

T775

�L7

76�

K777

�Y7

78�

F779

�G7

80�

S785

�Q7

86�

I787

L788

�P7

89�

D790

�P7

91�

L792

�K7

93�

P794

�T7

95�

K796

�R7

97�

S798

�F7

99�

I800

E801

�D8

02�

L803

�L8

04F8

05�

N806

�K8

07�

V808

�T8

09�

LEU

ALA

ASP

ALA

GLY

PHE

MET

LYS

Q818

�Y8

19�

G820

�E8

21�

C822

�L8

23�

G824

�AS

PIL

EAS

NAL

AAR

GAS

PL8

31�

I832

�C8

33�

A834

�Q8

35�

K836

�F8

37�

N838

G839

�

V842

�L8

43�

L846

�L8

47T8

48�

D849

�D8

50�

M851

�I8

52�

A853

�A8

54�

Y855

�T8

56�

A857

�A8

58�

L859

�V8

60�

S861

�

A864

�T8

65�

A866

�G8

67�

W868

�T8

69F8

70�

G871

A872

�G8

73�

A874

�A8

75�

L876

�Q8

77�

I878

�P8

79�

F880

�A8

81�

M882

�Q8

83�

M884

�A8

85�

Y886

�R8

87�

F888

�N8

89�

G890

�I8

91�

G892

�V8

93�

T894

�Q8

95�

N896

�V8

97�

L898

�Y8

99�

E900

�N9

01�

Q902

�K9

03�

Q904

�I9

05A9

06�

N907

�Q9

08�

F909

�N9

10�

K911

�A9

12I9

13�

S914

�Q9

15I9

16�

Q917

�E9

18�

S919

�L9

20�

T921

�T9

22�

T923

�

S924

�T9

25�

A926

L927

�G9

28�

K929

L930

�Q9

31�

D932

�V9

33V9

34�

N935

�Q9

36N9

37�

A938

�Q9

39�

A940

�L9

41�

N942

�T9

43L9

44�

V945

�K9

46�

Q947

�L9

48�

S949

�S9

50�

N951

�F9

52�

G953

�A9

54�

I955

�S9

56�

S957

�V9

58L9

59�

N960

�D9

61�

I962

�L9

63�

S964

�R9

65�

L966

�D9

67�

P968

�P9

69�

E970

�A9

71�

E972

�V9

73�

Q974

I975

�D9

76�

R977

�L9

78�

I979

�T9

80�

G981

R982

�L9

83�

Q984

�S9

85L9

86�

Q987

�T9

88Y9

89�

V990

Q993

�L9

94�

I995

R996

�A9

97�

A998

E999

�I1

000�

R100

1�

A100

2S1

003�

A100

4N1

005

L100

6�

A100

7�

A100

8�

T100

9K1

010�

E101

3C1

014�

V101

5L1

016�

G101

7Q1

018�

S101

9�

K102

0R1

021�

V102

2D1

023�

F102

4�

C102

5G1

026�

K102

7�

G102

8�

Y102

9H1

030�

L103

1�

M103

2�

S103

3F1

034�

P103

5Q1

036�

A103

7�

A103

8�

P103

9�

H104

0�

G104

1V1

042

V104

3�

F104

4�

L104

5�

H104

6�

V104

7�

T104

8�

Y104

9�

V105

0�

P105

1S1

052�

Q105

3�

E105

4�

R105

5�

N105

6�

T105

9�

A106

0�

P106

1�

A106

2�

I106

3�

C106

4�

G106

7�

K106

8�

A106

9�

Y107

0�

F107

1P1

072�

R107

3�

E107

4�

G107

5�

V107

6�

F107

7V1

078�

F107

9�

N108

0�

G108

1�

T108

2�

F108

5�

I108

6�

T108

7Q1

088�

R108

9�

N109

0�

F109

1�

F109

2�

S109

3�

P109

4�

Q109

5�

I109

6�

I109

7T1

098�

T109

9D1

100�

N110

1�

T110

2F1

103�

V110

4S1

105�

G110

6N1

107�

C110

8�

D110

9�

V111

0�

V111

1�

I111

2�

G111

3�

I111

4�

I111

5�

N111

6�

N111

7�

T111

8�

V111

9�

Y112

0�

ASP

PRO

LEU

GLN

PRO

GLU

LEU

ASP

SER

PHE

LYS

GLU

GLU

LEU

ASP

LYS

TYR

PHE

LYS

ASN

HIS

THR

SER

PRO

ASP

VAL

ASP

LEU

GLY

ASP

ILE

SER

GLY

ILE

ASN

ALA

SER

VAL

VAL

ASN

ILE

GLN

LYS

GLU

ILE

ASP

ARG

LEU

ASN

GLU

VAL

ALA

LYS

ASN

LEU

ASN

GLU

SER

LEU

ILE

ASP

LEU

GLN

GLU

LEU

GLY

LYS

TYR

GLU

GLN

GLY

SER

GLY

TYR

ILE

PRO

GLU

ALA

PRO

ARG

ASP

GLY

GLN

ALA

TYR

VAL

ARG

LYS

ASP

GLY

GLU

TRP

VAL

LEU

LEU

SER

THR

PHE

LEU

GLY

ARG

SER

LEU

GLU

VAL

LEU

PHE

GLN


Chain B:

SER

ASP

LEU

ASP

R18�

C19�

T20�

T21�

F22�

D23�

D24�

V25�

Q26�

A27�

P28�

N29�

Y30�

T31�

Q32�

H33�

T34�

S35�

S36�

M37�

R38�

G39�

V40�

Y41�

Y42�

P43�

D44�

E45�

I46�

F47�

R48�

S49�

D50�

T51�

L52�

Y53�

L54�

T55�

Q56�

D57�

L58�

F59�

L60

P61�

F62�

Y63�

S64�

N65�

V66�

T67

G68�

F69�

H70�

T71�

I72�

N73�

H74

�T7

5�

F76

�G7

7�

N78

�P7

9�

V80

�I8

1�

P82

�F8

3�

K84

�D8

5�

G86

�I8

7�

Y88

�F8

9�

A90

�A9

1�

T92

�E9

3�

K94

�S9

5�

N96

�V9

7�

V98

�R9

9�

G100

�W1

01V1

02�

F103

�G1

04�

S105

�T1

06�

M107

�N1

08�

N109

�K1

10�

S111

�Q1

12�

S113

�V1

14�

I115

�I1

16�

I117

�N1

18�

N119

�S1

20�

T121

�N1

22�

V123

�V1

24�

I125

�R1

26�

A127

�C1

28�

N129

�F1

30�

E131

�L1

32�

C133

�


D134

�N1

35�

P136

�F1

37�

F138

�A1

39�

V140

�S1

41�

K142

�P1

43�

M144

�G1

45�

T146

�Q1

47�

T148

�H1

49�

T150

�M1

51�

I152

�F1

53�

D154

�N1

55�

A156

�F1

57�

N158

�C1

59�

T160

�F1

61�

E162

�Y1

63�

I164

�S1

65�

D166

�A1

67�

F168

�S1

69�

L170

�D1

71�

V172

�S1

73�

E174

�K1

75�

S176

�G1

77�

N178

�F1

79�

K180

�H1

81�

L182

�R1

83�

E184

�F1

85�

V186

�F1

87�

K188

�N1

89�

K190

�D1

91�

G192

�F1

93�

L194

�Y1

95V1

96�

Y197

�K1

98�

G199

�Y2

00�

Q201

�P2

02�

I203

�D2

04�

V205

�V2

06�

R207

�D2

08�

L209

�P2

10�

S211

�G2

12�

F213

�N2

14�

T215

�L2

16�

K217

�P2

18I2

19�

F220

�K2

21�

L222

�P2

23�

L224

�G2

25I2

26�

N227

�I2

28�

T229

�N2

30�

F231

�R2

32�

A233

�I2

34�

L235

�T2

36�

A237

�F2

38�

S239

�P2

40�

ALA

GLN

ASP

I244

�W2

45�

G246

�T2

47�

S248

�A2

49�

A250

�A2

51�

Y252

�F2

53�

V254

�G2

55�

Y256

�L2

57�

K258

�P2

59�

T260

�T2

61�

F262

�M2

63�

L264

K265

�Y2

66�

D267

�E2

68�

N269

�G2

70�

T271

I272

�T2

73D2

74�

A275

�V2

76�

D277

�C2

78�

S279

�Q2

80�

N281

�P2

82�

L283

�A2

84E2

85�

L286

�K2

87�

C288

�S2

89�

V290

�K2

91�

S292

�F2

93�

E294

�I2

95�

D296

�K2

97�

G298

�I2

99�

Y300

�Q3

01�

T302

�S3

03�

N304

�F3

05�

R306

�V3

07�

V308

�P3

09�

S310

�G3

11�

D312

V313

�

V314

R315

�F3

16�

P317

�N3

18�

I319

�T3

20�

N321

�L3

22�

C323

�P3

24�

F325

�G3

26�

E327

�V3

28�

F329

�N3

30�

A331

�T3

32�

K333

�F3

34�

P335

�S3

36�

V337

�Y3

38�

A339

�W3

40�

E341

�R3

42�

K343

�K3

44�

I345

�S3

46�

N347

�C3

48�

V349

�A3

50�

D351

�Y3

52�

S353

�V3

54�

L355

�Y3

56�

N357

�S3

58�

T359

�F3

60�

F361

�S3

62�

T363

�F3

64�

K365

�C3

66�

Y367

�GL

YVA

LSE

RA3

71�

T372

�K3

73�

L374

�N3

75�

D376

�L3

77�

C378

�F3

79�

S380

�N3

81�

V382

�Y3

83�

A384

�D3

85�

S386

�F3

87�

V388

�V3

89�

K390

�G3

91�

D392

�D3

93�

V394

�R3

95�

Q396

�I3

97�

A398

�P3

99�

G400

�Q4

01�

T402

�G4

03�

V404

�I4

05�

A406

�D4

07�

Y408

�N4

09�

Y410

�K4

11�

L412

�P4

13�

D414

�D4

15�

F416

�M4

17�

G418

�C4

19�

V420

�L4

21�

A422

�W4

23�

N424

�T4

25�

R426

�N4

27�

I428

�D4

29�

A430

�T4

31�

S432

�T4

33�

G434

�N4

35�

Y436

�N4

37�

Y438

�K4

39�

Y440

�R4

41�

Y442

�L4

43�

R444

�H4

45�

G446

�K4

47�

L448

�R4

49�

P450

�F4

51�

E452

�R4

53�

D454

�I4

55�

S456

�N4

57�

V458

�P4

59�

F460

�S4

61�

P462

�D4

63�

G464

�K4

65�

P466

�C4

67�

T468

�P4

69�

P470

�A4

71�

L472

�N4

73�

C474

�Y4

75�

W476

�P4

77�

L478

�N4

79�

D480

�Y4

81�

G482

�F4

83�

Y484

�T4

85�

T486

�T4

87�

G488

�I4

89�

G490

�Y4

91�

Q492

�P4

93�

Y494

�R4

95�

V496

�V4

97�

V498

�L4

99�

S500

�F5

01�

E502

�LE

ULE

UAS

NAL

APR

OAL

AT5

09�

V510

�C5

11�

G512

�P5

13�

K514

L515

�S5

16�

T517

�D5

18�

L519

�I5

20�

K521

�N5

22�

Q523

�C5

24�

V525

�N5

26F5

27�

N528

F529

�N5

30�

G531

�L5

32�

T533

�G5

34�

T535

�G5

36V5

37�

L538

T539

�P5

40�

S541

�S5

42�

K543

�R5

44�

F545

�Q5

46�

P547

�F5

48�

Q549

�Q5

50�

F551

�G5

52�

R553

�

D554

�V5

55�

S556

�D5

57�

F558

�T5

59�

D560

�S5

61�

V562

�R5

63�

D564

�P5

65�

K566

�T5

67�

S568

�E5

69�

I570

�L5

71�

D572

�I5

73S5

74�

P575

�C5

76�

A577

�F5

78�

G579

�G5

80�

V581

�S5

82�

V583

�I5

84�

T585

P586

�

N589

�A5

90�

S591

�S5

92E5

93�

V594

�A5

95�

V596

�L5

97�

Y598

�Q5

99�

D600

�V6

01�

N602

�C6

03�

T604

�D6

05�

V606

�S6

07�

T608

�A6

09I6

10�

H611

�A6

12�

D613

�Q6

14�

L615

�T6

16�

P617

�A6

18�

W619

�R6

20�

I621

�Y6

22�

S623

�T6

24�

G625

�N6

26�

N627

�V6

28�

F629

�Q6

30�

T631

�Q6

32�

A633

G634

C635

�L6

36�

I637

�

H641

�V6

42D6

43�

T644

�S6

45�

Y646

�E6

47�

C648

�D6

49�

I650

�P6

51�

I652

�G6

53A6

54�

G655

�I6

56C6

57�

A658

�S6

59�

Y660

�H6

61T6

62�

V663

�SE

RLE

ULE

UAR

GSE

RTH

RSE

RGL

NK6

72�

S673

�I6

74V6

75�

A676

Y677

T678

�M6

79�

S680

L681

�G6

82�

A683

�D6

84�

S685

�S6

86�

I687

�A6

88�

Y689

�S6

90�

N691

�N6

92�

T693

I694

�A6

95�

I696

�P6

97�

T698

�N6

99F7

00�

S701

�I7

02�

E707

P710

V711

S712

�M7

13A7

14�

K715

�T7

16�

S717

�V7

18�

D719

�C7

20�

N721

�

I724

�C7

25�

G726

�D7

27�

S728

�T7

29E7

30�

C731

�A7

32�

N733

�L7

34�

L735

�L7

36Q7

37�

Y738

�G7

39�

S740

�F7

41�

C742

T743

�Q7

44�

L745

�N7

46�

R747

�A7

48�

L749

S750

�G7

51�

A754

�E7

55�

Q756

D757

�R7

58�

R761

�E7

62�

V763

F764

�A7

65�

Q766

�V7

67�

K768

�Q7

69�

M770

�Y7

71�

K772

�T7

73�

P774

T775

�L7

76K7

77�

Y778

F779

�

F782

�N7

83F7

84�

I787

�L7

88�

P789

�D7

90�

P791

�L7

92�

K793

�P7

94�

T795

�K7

96�

R797

S798

�F7

99I8

00�

E801

�

L804

�F8

05�

N806

K807

V808

�T8

09�

LEU

ALA

ASP

ALA

GLY

PHE

MET

LYS

Q818

�Y8

19�

G820

�E8

21�

C822

�L8

23�

GLY

ASP

ILE

ASN

ALA

ARG

ASP

L831

�I8

32�

C833

�

K836

�F8

37�

N838

�G8

39�

L840

�T8

41�

V842

L843

�P8

44P8

45�

L846

�L8

47�

T848

�D8

49�

D850

M851

�

A854

�Y8

55�

A858

�L8

59�

V860

S861

�G8

62�

T863

�A8

64T8

65�

A866

�G8

67W8

68�

T869

�

F870

�G8

71�

A872

�G8

73�

A874

�A8

75�

L876

�Q8

77�

I878

�P8

79F8

80�

A881

M882

�Q8

83�

M884

�A8

85Y8

86�

R887

�F8

88N8

89�

G890

�I8

91G8

92�

V893

�T8

94�

V897

�L8

98�

Y899

E900

N901

�Q9

02�

I905

�A9

06�

N910

�K9

11A9

12�

I913

�S9

14Q9

15�

T922

�T9

23�

S924

�T9

25�

A926

�

K929

�L9

30Q9

31�

D932

�

Q936

�N9

37�

A938

Q939

�A9

40�

T943

�L9

44�

V945

�K9

46�

Q947

�L9

48�

S949

�S9

50�

N951

�F9

52�

G953

�A9

54�

I955

�S9

56�

S957

�V9

58�

L959

�N9

60�

D961

�I9

62�

L963

�S9

64�

R965

�L9

66�

D967

�P9

68�

P969

�E9

70�

A971

�E9

72�

V973

�Q9

74�

I975

D976

�R9

77�

L978

�I9

79T9

80�

G981

�R9

82�

L983

�Q9

84�

S985

�L9

86Q9

87�

T988

�

Q992

�Q9

93L9

94�

I995

R996

A997

A998

�E9

99�

I100

0R1

001�

A100

8�

T100

9


K101

0M1

011�

S101

2E1

013�

C101

4V1

015�

L101

6G1

017�

Q101

8S1

019�

K102

0�

R102

1V1

022�

D102

3�

K102

7�

G102

8�

Y102

9�

H103

0�

L103

1�

M103

2�

S103

3�

F103

4

A103

8�

P103

9H1

040�

G104

1V1

042�

L104

5H1

046

V104

7�

T104

8Y1

049�

Q105

3�

E105

4�

R105

5�

N105

6�

F105

7�

T105

8�

T105

9�

A106

0P1

061�

A106

2�

I106

3�

C106

4�

H106

5�

E106

6�

G106

7�

K106

8�

A106

9Y1

070�

F107

1�

P107

2�

R107

3�

E107

4�

G107

5V1

076�

F107

7V1

078�

F107

9N1

080�

G108

1�

T108

2S1

083

W108

4�

F108

5I1

086�

T108

7�

Q108

8�

R108

9�

N109

0�

F109

1�

F109

2�

S109

3�

P109

4Q1

095�

I109

6�

I109

7�

T109

8�

T109

9�

D110

0�

N110

1�

T110

2F1

103�

V110

4�

S110

5�

G110

6�

N110

7�

C110

8D1

109�

V111

0�

V111

1�

I111

2�

G111

3�

I111

4�

I111

5N1

116�

N111

7�

T111

8�

V111

9�

Y112

0�

ASP

PRO

LEU

GLN

PRO

GLU

LEU

ASP

SER

PHE

LYS

GLU

GLU

LEU

ASP

LYS

TYR

PHE

LYS

ASN

HIS

THR

SER

PRO

ASP

VAL

ASP

LEU

GLY

ASP

ILE

SER

GLY

ILE

ASN

ALA

SER

VAL

VAL

ASN

ILE

GLN

LYS

GLU

ILE

ASP

ARG

LEU

ASN

GLU

VAL

ALA

LYS

ASN

LEU

ASN

GLU

SER

LEU

ILE

ASP

LEU

GLN

GLU

LEU

GLY

LYS

TYR

GLU

GLN

GLY

SER

GLY

TYR

ILE

PRO

GLU

ALA

PRO

ARG

ASP

GLY

GLN

ALA

TYR

VAL

ARG

LYS

ASP

GLY

GLU

TRP

VAL

LEU

LEU

SER

THR

PHE

LEU

GLY

ARG

SER

LEU

GLU

VAL

LEU

PHE

GLN


Chain C:

SER

ASP

LEU

ASP

R18�

C19�

T20�

T21�

F22�

D23�

D24�

V25�

Q26�

A27�

P28�

N29�

Y30�

T31�

Q32�

H33�

T34�

S35�

S36�

M37�

R38�

G39

V40�

Y41�

Y42�

P43

D44�

E45�

I46�

F47�

R48�

S49�

D50�

T51�

L52�

Y53

L54�

T55�

Q56�

D57�

L58�

F59�

L60�

P61�

F62�

Y63�

S64�

N65�

V66�

T67�

G68�

F69

H70�

T71�

I72�

N73�

H74

�T7

5�

F76

�G7

7�

N78

�P7

9V8

0�

I81

�P8

2F8

3�

K84

�D8

5�

G86

I87

�Y8

8�

F89

�A9

0A9

1�

T92

�E9

3�

K94

�S9

5�

N96

�V9

7�

V98

�R9

9�

G100

�W1

01�

V102

�F1

03�

G104

�S1

05�

T106

�M1

07�

N108

�N1

09�

K110

�S1

11�

Q112

�S1

13�

V114

I115

�I1

16�

I117

�N1

18�

N119

�S1

20�

T121

�N1

22�

V123

�V1

24�

I125

�R1

26�

A127

�C1

28�

N129

�F1

30�

E131

�L1

32�

C133

�

D134

�N1

35�

P136

�F1

37�

F138

�A1

39�

V140

�S1

41�

K142

�P1

43�

M144

�G1

45�

T146

�Q1

47�

T148

�H1

49�

T150

�M1

51�

I152

�F1

53�

D154

�N1

55�

A156

�F1

57�

N158

�C1

59�

T160

�F1

61�

E162

�Y1

63�

I164

�S1

65�

D166

�A1

67�

F168

�S1

69�

L170

�D1

71�

V172

�S1

73�

E174

�K1

75�

S176

�G1

77�

N178

�F1

79�

K180

�H1

81�

L182

�R1

83�

E184

�F1

85�

V186

F187

�K1

88�

N189

�K1

90�

D191

�G1

92�

F193

�

L194

�Y1

95V1

96�

Y197

K198

�G1

99Y2

00�

Q201

�P2

02�

I203

�D2

04�

V205

�V2

06�

R207

�D2

08�

L209

�P2

10�

S211

�G2

12�

F213

�N2

14�

T215

�L2

16�

K217

�P2

18�

I219

�F2

20�

K221

�L2

22�

P223

�L2

24�

G225

�I2

26�

N227

�I2

28�

F231

�R2

32�

A233

�I2

34�

L235

�T2

36�

A237

�F2

38�

S239

�P2

40�

ALA

GLN

ASP

I244

�W2

45�

G246

�T2

47�

S248

�A2

49�

A250

�A2

51�

Y252

�

G255

�

Y256

�L2

57�

K258

�P2

59T2

60�

T261

F262

�M2

63�

L264

�K2

65�

Y266

�D2

67�

E268

�N2

69�

G270

T271

�I2

72�

T273

�D2

74�

A275

�V2

76�

D277

�C2

78S2

79�

Q280

�N2

81�

P282

L283

�A2

84�

E285

�L2

86�

K287

C288

�S2

89�

V290

�

F293

�E2

94�

I295

�D2

96�

K297

�G2

98�

I299

�Y3

00�

Q301

�T3

02S3

03�

N304

�F3

05�

R306

�V3

07�

V308

�P3

09�

S310

�G3

11�

D312

�V3

13�

V314

�R3

15�

F316

�

P317

�N3

18�

I319

�T3

20�

N321

�L3

22�

C323

�P3

24�

F325

�G3

26�

E327

�V3

28�

F329

�N3

30�

A331

�T3

32�

K333

�F3

34�

P335

�S3

36�

V337

�Y3

38�

A339

�W3

40�

E341

�R3

42�

K343

�K3

44�

I345

�S3

46�

N347

�C3

48�

V349

�A3

50�

D351

�Y3

52�

S353

�V3

54�

L355

�Y3

56�

N357

�S3

58�

T359

�F3

60�

F361

�S3

62�

T363

�F3

64�

K365

�C3

66�

TYR

GLY

VAL

SER

A371

�T3

72�

K373

�L3

74�

N375

�D3

76�

L377

�C3

78�

F379

�S3

80�

N381

�V3

82�

Y383

�A3

84�

D385

�S3

86�

F387

�V3

88�

V389

�K3

90�

G391

�D3

92�

D393

�V3

94�

R395

�Q3

96�

I397

�A3

98�

P399

�G4

00�

Q401

�T4

02�

G403

�V4

04�

I405

�A4

06�

D407

�Y4

08�

N409

�Y4

10�

K411

�L4

12�

P413

�D4

14�

D415

�F4

16�

M417

�G4

18�

C419

�V4

20�

L421

�A4

22�

W423

�N4

24�

T425

�R4

26�

N427

�I4

28�

D429

�A4

30�

T431

�S4

32�

T433

�G4

34�

N435

�Y4

36�

N437

�Y4

38�

K439

�Y4

40�

R441

�Y4

42�

L443

�R4

44�

H445

�G4

46�

K447

�L4

48�

R449

�P4

50�

F451

�E4

52�

R453

�D4

54�

I455

�S4

56�

N457

�V4

58�

P459

�F4

60�

S461

�P4

62�

D463

�G4

64�

K465

�P4

66�

C467

�T4

68�

P469

�P4

70�

A471

�L4

72�

N473

�C4

74�

Y475

�W4

76�

P477

�L4

78�

N479

�D4

80�

Y481

�G4

82�

F483

�Y4

84�

T485

�T4

86�

T487

�G4

88�

I489

�G4

90�

Y491

�Q4

92�

P493

�Y4

94�

R495

�V4

96�

V497

�V4

98�

L499

�S5

00�

F501

�E5

02�

LEU

LEU

ASN

ALA

PRO

ALA

T509

�V5

10�

C511

�G5

12�

P513

�K5

14�

L515

�S5

16�

T517

�D5

18�

L519

�I5

20�

K521

�N5

22�

Q523

�C5

24�

V525

�N5

26�

F527

�N5

28�

F529

�N5

30�

G531

�L5

32�

T533

�G5

34�

T535

�G5

36�

V537

�L5

38�

T539

�P5

40�

S541

�S5

42�

K543

�R5

44�

F545

�Q5

46P5

47�

F548

�Q5

49�

Q550

�F5

51�

G552

�R5

53�

D554

�V5

55S5

56�


D557

�F5

58�

T559

�D5

60S5

61�

V562

�R5

63�

D564

�P5

65�

K566

�T5

67�

S568

�E5

69�

I570

L571

�D5

72�

I573

�S5

74�

P575

C576

�A5

77�

F578

G579

�

I584

�T5

85�

P586

G587

�T5

88�

N589

�A5

90�

S591

�S5

92�

E593

�V5

94�

A595

�V5

96�

L597

Y598

�Q5

99�

D600

V601

N602

�C6

03�

T604

�D6

05�

V606

S607

�T6

08�

A609

�I6

10�

H611

�A6

12�

D613

�Q6

14L6

15�

T616

�P6

17A6

18�

W619

�

R620

�I6

21�

Y622

�S6

23�

T624

�G6

25�

N626

�N6

27V6

28�

F629

�Q6

30�

T631

Q632

�A6

33�

G634

C635

�L6

36I6

37�

G638

�A6

39�

E640

�H6

41�

V642

�D6

43�

T644

S645

�Y6

46E6

47�

C648

�D6

49�

I650

�P6

51I6

52�

G653

�A6

54�

A658

�S6

59�

Y660

�H6

61�

T662

�VA

LSE

RLE

ULE

UAR

GSE

RTH

RSE

RGL

NK6

72�

S673

�I6

74�

V675

�A6

76�

Y677

T678

�M6

79S6

80�

L681

�

G682

�A6

83�

D684

�S6

85�

S686

�I6

87�

A688

�Y6

89�

S690

�N6

91�

N692

�T6

93�

I694

�A6

95�

I696

P697

�T6

98�

N699

�F7

00S7

01�

I702

�S7

03�

I704

T705

�T7

06�

E707

�V7

08�

M709

�

S712

�M7

13�

A714

�K7

15�

T716

�S7

17�

V718

�D7

19�

C720

N721

�M7

22�

Y723

�I7

24C7

25�

G726

�D7

27�

S728

�T7

29�

E730

�C7

31�

A732

�N7

33�

L734

�L7

35�

L736

�Q7

37�

Y738

�G7

39�

S740

�F7

41�

C742

�

T743

�Q7

44L7

45�

N746

�R7

47�

A748

L749

�S7

50�

A753

�A7

54�

E755

Q756

�D7

57�

R761

�

F764

�A7

65Q7

66

Q769

�M7

70Y7

71�

K772

�T7

73P7

74�

T775

L776

�K7

77�

Y778

�F7

79�

G780

�G7

81�

F782

�N7

83�

F784

�S7

85�

Q786

�I7

87L7

88�

P789

D790

�P7

91L7

92�

K793

�P7

94�

T795

�K7

96�

R797

�S7

98F7

99�

I800

�E8

01�

D802

�L8

03�

L804

F805

N806

�K8

07�

V808

T809

�LE

UAL

AAS

PAL

AGL

YPH

EME

TLY

SQ8

18Y8

19�

G820

�E8

21�

C822

L823

�G8

24�

D825

�I8

26�

ASN

ALA

ARG

ASP

L831

�I8

32�

C833

�A8

34�

Q835

�K8

36�

F837

�N8

38�

G839

�L8

40�

T841

�V8

42�

L843

P844

�P8

45�

L846

L847

�T8

48D8

49�

D850

�M8

51I8

52A8

53�

T856

�A8

57�

A858

L859

�V8

60�

S861

G862

T863

�A8

64�

T865

�A8

66�

G867

�W8

68�

T869

�F8

70�

G871

�A8

72G8

73�

A874

�A8

75�

L876

�Q8

77I8

78�

P879

�F8

80�

A881

�M8

82�

Q883

M884

�A8

85�

Y886

�R8

87�

F888

�N8

89�

G890

I891

�G8

92�

V893

�T8

94�

Q895

�N8

96�

V897

�L8

98Y8

99�

E900

�N9

01�

Q902

K903

�Q9

04�

I905

�A9

06N9

07�

Q908

�F9

09�

N910

�K9

11�

A912

�

Q915

�

E918

�S9

19�

L920

T921

�T9

22�

T923

�S9

24�

T925

�A9

26�

L927

�G9

28�

K929

�L9

30�

Q931

�D9

32�

V933

V934

�

A938

�Q9

39�

A940

L941

�N9

42�

V945

�K9

46�

Q947

L948

�S9

49�

S950

�N9

51�

F952

�G9

53�

A954

�I9

55�

S956

�S9

57�

V958

�L9

59�

N960

�D9

61�

I962

�L9

63�

S964

�R9

65�

L966

�D9

67�

P968

�P9

69�

E970

�A9

71�

E972

�V9

73Q9

74�

I975

�D9

76�

R977

�L9

78�

I979

�T9

80G9

81�

R982

�L9

83�

Q984

�S9

85�

L986

�Q9

87T9

88�

Y989

V990

T991

Q992

�Q9

93�

L994

I995

�R9

96�

A997

�A9

98E9

99I1

000�

R100

1A1

002�

S101

2E1

013�

C101

4V1

015�

L101

6G1

017�

Q101

8�

S101

9�

K102

0R1

021�

V102

2�

D102

3�

K102

7�

G102

8�

Y102

9�

H103

0L1

031�

M103

2�

S103

3�

F103

4�

P103

5Q1

036�

A103

7�

H104

0�

G104

1�

V104

2�

V104

3�

F104

4�

L104

5�

H104

6�

V104

7T1

048�

Y104

9V1

050�

P105

1�

S105

2�

Q105

3�

E105

4�

R105

5�

N105

6�

F105

7�

T105

8�

T105

9�

A106

0�

P106

1A1

062�

I106

3�

C106

4�

H106

5E1

066�

G106

7�

K106

8�

A106

9�

Y107

0�

F107

1�

P107

2�

R107

3E1

074

G107

5�

V107

6�

F107

7�

V107

8�

F107

9�

N108

0�

G108

1�

T108

2�

S108

3W1

084�

F108

5�

I108

6�

T108

7�

Q108

8�

R108

9�

N109

0�

F109

1�

F109

2�

S109

3�

P109

4�

Q109

5I1

096�

I109

7�

T109

8T1

099�

D110

0�

N110

1�

T110

2�

F110

3�

V110

4�

S110

5�

G110

6�

N110

7�

C110

8�

D110

9�

V111

0�

V111

1�

I111

2�

G111

3�

I111

4�

I111

5�

N111

6�

N111

7�

T111

8�

V111

9�

Y112

0AS

PPR

OLE

UGL

N

PRO

GLU

LEU

ASP

SER

PHE

LYS

GLU

GLU

LEU

ASP

LYS

TYR

PHE

LYS

ASN

HIS

THR

SER

PRO

ASP

VAL

ASP

LEU

GLY

ASP

ILE

SER

GLY

ILE

ASN

ALA

SER

VAL

VAL

ASN

ILE

GLN

LYS

GLU

ILE

ASP

ARG

LEU

ASN

GLU

VAL

ALA

LYS

ASN

LEU

ASN

GLU

SER

LEU

ILE

ASP

LEU

GLN

GLU

LEU

GLY

LYS

TYR

GLU

GLN

GLY

SER

GLY

TYR

ILE

PRO

GLU

ALA

PRO

ARG

ASP

GLY

GLN

ALA

TYR

VAL

ARG

LYS

ASP

GLY

GLU

TRP

VAL

LEU

LEU

SER

THR

PHE

LEU

GLY

ARG

SER

LEU

GLU

VAL

LEU

PHE

GLN

• Molecule 2: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Chain D:

NAG1

�NA

G2�

BMA3

�



Chain F:NA

G1�

NAG2

�BM

A3�


Chain J:

NAG1

�NA

G2�

BMA3

�


Chain K:

NAG1

�NA

G2�

BMA3

�


Chain M:

NAG1

�NA

G2�

BMA3

�


Chain N:

NAG1

NAG2

�BM

A3�


Chain R:

NAG1

�NA

G2�

BMA3

�



Chain T:

NAG1

�NA

G2�

BMA3

�


Chain U:

NAG1

�NA

G2�

BMA3

�

• Molecule 3: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Chain E:

NAG1

�NA

G2�

BMA3

�MA

N4�

• Molecule 4: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Chain G:

NAG1

�NA

G2�


Chain H:

NAG1

�NA

G2�


Chain I:


NAG1

�NA

G2�


Chain L:

NAG1

�NA

G2�


Chain O:

NAG1

�NA

G2�


Chain P:

NAG1

�NA

G2�


Chain Q:

NAG1

�NA

G2�


Chain V:

NAG1

�NA

G2�

• Molecule 5: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Chain S:NA

G1�

NAG2

�BM

A3�

MAN4

�


4 Experimental information i○

Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, C3 DepositorNumber of particles used 162177 DepositorResolution determination method FSC 0.143 CUT-OFF DepositorCTF correction method PHASE FLIPPING AND AMPLITUDE

CORRECTIONDepositor

Microscope FEI TITAN KRIOS DepositorVoltage (kV) 300 DepositorElectron dose (e−/Å2

) 65 DepositorMinimum defocus (nm) 1200 DepositorMaximum defocus (nm) 2200 DepositorMagnification 29000 DepositorImage detector GATAN K2 SUMMIT (4k x 4k) DepositorMaximum map value 0.374 DepositorMinimum map value -0.191 DepositorAverage map value -0.000 DepositorMap value standard deviation 0.008 DepositorRecommended contour level 0.069 DepositorMap size (Å) 329.59998, 329.59998, 329.59998 wwPDBMap dimensions 320, 320, 320 wwPDBMap angles (◦) 90.0, 90.0, 90.0 wwPDBPixel spacing (Å) 1.03, 1.03, 1.03 Depositor

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#experimental_info


5 Model quality i○

5.1 Standard geometry i○

Bond lengths and bond angles in the following residue types are not validated in this section:BMA, NAG, MAN

The Z score for a bond length (or angle) is the number of standard deviations the observed valueis removed from the expected value. A bond length (or angle) with |Z| > 5 is considered anoutlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (orangles).

Mol Chain Bond lengths Bond anglesRMSZ #|Z| >5 RMSZ #|Z| >5

1 A 0.37 0/8538 0.59 2/11617 (0.0%)1 B 0.37 0/8541 0.59 1/11622 (0.0%)1 C 0.37 0/8541 0.59 0/11621All All 0.37 0/25620 0.59 3/34860 (0.0%)

Chiral center outliers are detected by calculating the chiral volume of a chiral center and verifying ifthe center is modelled as a planar moiety or with the opposite hand.A planarity outlier is detectedby checking planarity of atoms in a peptide group, atoms in a mainchain group or atoms of asidechain that are expected to be planar.

Mol Chain #Chirality outliers #Planarity outliers1 A 0 11 B 0 11 C 0 3All All 0 5

There are no bond length outliers.

All (3) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 B 1070 TYR C-N-CA 5.77 136.12 121.701 A 355 LEU CA-CB-CG 5.28 127.44 115.301 A 898 LEU CB-CG-CD1 -5.25 102.08 111.00

There are no chirality outliers.

All (5) planarity outliers are listed below:

Mol Chain Res Type Group1 A 85 ASP Peptide


https://www.wwpdb.org/validation/2017/EMValidationReportHelp#model_quality

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#standard_geometry


Continued from previous page...Mol Chain Res Type Group1 B 1080 ASN Peptide1 C 207 ARG Peptide1 C 525 VAL Peptide1 C 85 ASP Peptide

5.2 Too-close contacts i○

In the following table, the Non-H and H(model) columns list the number of non-hydrogen atomsand hydrogen atoms in the chain respectively. The H(added) column lists the number of hydrogenatoms added and optimized by MolProbity. The Clashes column lists the number of clashes withinthe asymmetric unit, whereas Symm-Clashes lists symmetry-related clashes.

Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes1 A 8339 0 8083 133 01 B 8342 0 8088 113 01 C 8343 0 8086 118 02 D 39 0 34 0 02 F 39 0 34 0 02 J 39 0 34 0 02 K 39 0 34 0 02 M 39 0 34 0 02 N 39 0 34 0 02 R 39 0 34 0 02 T 39 0 34 0 02 U 39 0 34 0 03 E 50 0 43 0 04 G 28 0 25 1 04 H 28 0 25 0 04 I 28 0 25 0 04 L 28 0 25 0 04 O 28 0 25 0 04 P 28 0 25 0 04 Q 28 0 25 0 04 V 28 0 25 0 05 S 50 0 43 0 06 A 56 0 52 1 06 B 70 0 65 1 06 C 84 0 78 0 0All All 25909 0 25044 344 0

The all-atom clashscore is defined as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 7.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#close_contacts


All (344) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:C:405:ILE:HA 1:C:409:ASN:HB2 1.74 0.701:A:1034:PHE:HB2 1:A:1045:LEU:HB2 1.77 0.671:C:444:ARG:HE 1:C:454:ASP:HB2 1.60 0.671:A:188:LYS:HB3 1:A:195:TYR:HB2 1.76 0.661:A:227:ASN:HB2 1:C:444:ARG:HH22 1.61 0.661:A:99:ARG:HH22 1:A:172:VAL:HA 1.60 0.661:B:337:VAL:HG22 1:B:387:PHE:HB2 1.78 0.651:A:334:PHE:HB2 1:A:388:VAL:HG23 1.78 0.651:B:1018:GLN:NE2 1:B:1030:HIS:O 2.29 0.651:C:285:GLU:OE1 1:C:619:TRP:NE1 2.30 0.651:C:341:GLU:HB3 1:C:386:SER:HB3 1.79 0.651:B:563:ARG:HA 1:B:570:ILE:HA 1.80 0.631:A:704:ILE:HG12 1:A:1047:VAL:HG22 1.79 0.631:B:93:GLU:HG3 1:B:183:ARG:HH21 1.64 0.631:C:366:CYS:SG 1:C:373:LYS:NZ 2.72 0.631:A:441:ARG:NH2 1:A:456:SER:O 2.32 0.621:A:99:ARG:HB3 1:A:118:ASN:HB3 1.80 0.621:A:99:ARG:HH12 1:A:172:VAL:HG12 1.65 0.621:A:126:ARG:NH2 1:A:159:CYS:SG 2.73 0.621:C:1068:LYS:HB3 1:C:1104:VAL:HG21 1.82 0.611:C:349:VAL:HG12 1:C:511:CYS:H 1.65 0.611:B:1034:PHE:HB2 1:B:1045:LEU:HB2 1.83 0.611:B:707:GLU:OE2 1:B:1010:LYS:NZ 2.33 0.611:C:355:LEU:HD22 1:C:419:CYS:HB2 1.82 0.611:C:188:LYS:HB2 1:C:195:TYR:HB2 1.81 0.611:C:325:PHE:HB3 1:C:328:VAL:HB 1.83 0.601:B:993:GLN:OE1 1:B:996:ARG:NH1 2.35 0.601:C:323:CYS:N 1:C:348:CYS:SG 2.74 0.601:A:26:GLN:HB2 1:A:75:THR:HA 1.84 0.601:A:18:ARG:HB2 1:A:151:MET:HG2 1.82 0.601:A:1036:GLN:HB2 1:A:1043:VAL:HB 1.83 0.601:B:142:LYS:HE2 1:B:240:PRO:HD3 1.83 0.601:A:541:SER:HB3 1:A:570:ILE:HG22 1.84 0.591:A:898:LEU:HD23 1:A:905:ILE:HD13 1.84 0.591:C:355:LEU:HD11 1:C:499:LEU:HD22 1.84 0.591:A:99:ARG:NH2 1:A:171:ASP:O 2.35 0.591:B:377:LEU:O 1:B:512:GLY:N 2.35 0.59

1:A:1001:ARG:NH2 1:C:999:GLU:OE2 2.36 0.591:A:415:ASP:O 1:B:965:ARG:NH2 2.36 0.59

1:B:716:THR:HG22 1:B:842:VAL:HG22 1.85 0.58Continued on next page...


Continued from previous page...


Clashoverlap (Å)

1:A:511:CYS:HB3 1:A:514:LYS:HD2 1.83 0.581:A:708:VAL:HG12 1:A:1043:VAL:HG22 1.86 0.581:C:716:THR:HG22 1:C:842:VAL:HG22 1.85 0.581:B:138:PHE:HB2 1:B:236:THR:HA 1.86 0.581:B:323:CYS:N 1:B:348:CYS:SG 2.77 0.581:C:70:HIS:HA 1:C:251:ALA:HA 1.85 0.58

1:B:152:ILE:HD13 1:B:234:ILE:HD13 1.85 0.581:C:186:VAL:HB 1:C:197:TYR:HB2 1.86 0.57

1:C:425:THR:HG21 1:C:495:ARG:HE 1.67 0.571:A:1086:ILE:HB 1:A:1095:GLN:HB2 1.86 0.571:B:550:GLN:OE1 1:B:563:ARG:NH2 2.37 0.571:A:1078:VAL:HG21 1:A:1087:THR:HG22 1.86 0.571:B:38:ARG:NH1 1:B:184:GLU:OE2 2.38 0.571:B:388:VAL:HG22 1:B:495:ARG:HG2 1.86 0.561:A:126:ARG:HB2 1:A:130:PHE:HZ 1.69 0.561:A:529:PHE:HB2 1:A:532:LEU:HB3 1.87 0.561:C:862:GLY:O 1:C:866:ALA:N 2.38 0.561:C:402:THR:HA 1:C:406:ALA:HB3 1.87 0.561:A:628:VAL:HG22 1:A:637:ILE:HG12 1.88 0.561:A:1038:ALA:HB2 1:A:1043:VAL:HG23 1.88 0.561:C:389:VAL:HG11 1:C:397:ILE:HD11 1.87 0.56

1:A:78:ASN:O 1:A:232:ARG:NH1 2.38 0.561:B:416:PHE:HB3 1:B:502:GLU:HB2 1.87 0.561:A:239:SER:HB3 1:A:246:GLY:H 1.70 0.561:A:354:VAL:HA 1:A:357:ASN:HB2 1.87 0.561:A:984:GLN:OE1 1:B:984:GLN:NE2 2.34 0.561:B:277:ASP:OD2 1:B:280:GLN:NE2 2.35 0.561:C:529:PHE:HB2 1:C:532:LEU:HB2 1.87 0.561:C:563:ARG:HA 1:C:570:ILE:HA 1.87 0.551:B:206:VAL:HG12 1:B:207:ARG:HG3 1.88 0.551:B:99:ARG:HH22 1:B:120:SER:HA 1.71 0.551:C:194:LEU:HD23 1:C:222:LEU:HD12 1.88 0.551:C:777:LYS:HD3 1:C:785:SER:HA 1.88 0.551:A:277:ASP:HB3 1:A:280:GLN:HG2 1.88 0.551:A:453:ARG:NH2 1:B:158:ASN:O 2.39 0.551:B:409:ASN:HD21 1:B:440:TYR:HB2 1.72 0.551:C:125:ILE:HB 1:C:163:TYR:HB3 1.89 0.551:C:92:THR:HB 1:C:251:ALA:HB3 1.88 0.551:A:824:GLY:HA3 1:A:831:LEU:HA 1.89 0.551:C:239:SER:HB3 1:C:246:GLY:H 1.71 0.551:B:383:TYR:HB2 1:B:500:SER:HB3 1.88 0.54





Clashoverlap (Å)

1:C:351:ASP:HB3 1:C:513:PRO:HD3 1.88 0.541:C:96:ASN:O 1:C:99:ARG:NH1 2.41 0.541:A:404:VAL:O 1:A:409:ASN:ND2 2.41 0.54

1:A:1029:TYR:HB2 1:A:1049:TYR:HB3 1.90 0.541:C:409:ASN:HD21 1:C:440:TYR:HB2 1.72 0.541:A:381:ASN:OD1 1:A:509:THR:N 2.41 0.541:B:999:GLU:OE2 1:C:1001:ARG:NH2 2.40 0.541:A:109:ASN:O 1:A:129:ASN:ND2 2.41 0.541:B:953:GLY:O 1:B:977:ARG:NH1 2.41 0.54

1:C:745:LEU:HD22 1:C:990:VAL:HG21 1.89 0.541:A:116:ILE:HA 1:A:125:ILE:HG12 1.90 0.531:A:149:HIS:HB3 1:A:151:MET:HG3 1.90 0.531:C:340:TRP:HE1 1:C:453:ARG:HB3 1.73 0.531:C:99:ARG:HB3 1:C:118:ASN:HB3 1.90 0.531:A:383:TYR:HB2 1:A:500:SER:HB3 1.89 0.531:B:78:ASN:ND2 1:B:136:PRO:O 2.42 0.531:A:25:VAL:HG23 1:A:76:PHE:HB2 1.89 0.531:C:906:ALA:O 1:C:910:ASN:ND2 2.42 0.53

1:A:758:ARG:NH1 1:A:762:GLU:OE2 2.42 0.531:C:1029:TYR:HB2 1:C:1049:TYR:HB3 1.91 0.531:B:419:CYS:H 1:B:499:LEU:HB2 1.74 0.531:C:353:SER:HA 1:C:356:TYR:HB3 1.90 0.531:A:737:GLN:OE1 1:C:951:ASN:ND2 2.39 0.531:A:955:ILE:HG23 1:A:962:ILE:HG12 1.91 0.531:A:182:LEU:HB2 1:A:203:ILE:HD13 1.91 0.531:C:327:GLU:HG2 1:C:328:VAL:HG23 1.90 0.531:A:126:ARG:HG2 1:A:162:GLU:HG3 1.91 0.531:B:1068:LYS:HA 1:B:1107:ASN:HA 1.89 0.531:C:783:ASN:N 1:C:910:ASN:OD1 2.42 0.52

1:A:139:ALA:HB3 1:A:149:HIS:HB2 1.91 0.521:B:1063:ILE:HD11 1:B:1097:ILE:HD13 1.91 0.521:A:896:ASN:O 1:A:900:GLU:N 2.38 0.52

1:A:425:THR:OG1 1:A:493:PRO:O 2.27 0.521:A:71:THR:HB 1:A:250:ALA:HB3 1.92 0.521:A:778:TYR:HB3 4:G:1:NAG:H81 1.90 0.521:A:337:VAL:HG11 1:A:405:ILE:HD12 1.92 0.521:B:887:ARG:NH1 1:B:1031:LEU:O 2.43 0.521:C:299:ILE:HG12 1:C:584:ILE:HG12 1.90 0.521:C:373:LYS:NZ 1:C:419:CYS:SG 2.79 0.521:A:378:CYS:HA 1:A:511:CYS:HA 1.92 0.521:B:642:VAL:HB 1:B:677:TYR:HB3 1.91 0.52





Clashoverlap (Å)

1:B:690:SER:OG 1:B:692:ASN:OD1 2.27 0.521:B:398:ALA:HB3 1:B:401:GLN:HG3 1.91 0.511:A:1030:HIS:NE2 1:A:1032:MET:O 2.44 0.511:B:1080:ASN:HB2 1:B:1085:PHE:HE1 1.75 0.511:B:883:GLN:HE21 1:B:887:ARG:HE 1.58 0.511:A:390:LYS:HD3 1:A:481:TYR:HB3 1.92 0.511:B:32:GLN:HG3 6:B:1301:NAG:H3 1.92 0.511:B:429:ASP:OD1 1:B:495:ARG:NH2 2.42 0.511:A:1112:ILE:HG23 6:A:1310:NAG:H62 1.93 0.511:B:99:ARG:HB2 1:B:138:PHE:HE2 1.76 0.511:A:380:SER:OG 1:A:381:ASN:N 2.44 0.511:A:297:LYS:HG3 1:A:586:PRO:HA 1.93 0.501:A:1086:ILE:HG12 1:A:1097:ILE:HG12 1.94 0.501:A:94:LYS:HB3 1:A:179:PHE:HA 1.92 0.501:B:282:PRO:HB2 1:B:594:VAL:HG21 1.92 0.501:C:930:LEU:HD21 1:C:1041:GLY:HA3 1.93 0.501:B:822:CYS:HA 1:B:833:CYS:HA 1.92 0.501:C:340:TRP:NE1 1:C:453:ARG:HB3 2.27 0.501:A:405:ILE:HA 1:A:409:ASN:HB2 1.94 0.501:B:459:PRO:HD2 1:B:469:PRO:HB2 1.94 0.501:B:762:GLU:O 1:B:766:GLN:NE2 2.39 0.501:C:62:PHE:O 1:C:620:ARG:NH2 2.45 0.50

1:A:184:GLU:HG2 1:A:216:LEU:HD21 1.94 0.501:A:366:CYS:HA 1:A:419:CYS:HA 1.93 0.501:A:818:GLN:O 1:A:838:ASN:ND2 2.44 0.50

1:A:337:VAL:HG22 1:A:387:PHE:HB2 1.92 0.491:A:711:VAL:HG12 1:A:1004:ALA:HA 1.93 0.491:A:764:PHE:HE2 1:A:852:ILE:HG23 1.78 0.491:B:405:ILE:HA 1:B:409:ASN:HB2 1.93 0.49

1:C:1057:PHE:HB3 1:C:1078:VAL:HB 1.94 0.491:A:112:GLN:HE22 1:C:453:ARG:HH21 1.60 0.491:B:316:PHE:HB3 1:B:513:PRO:HB2 1.94 0.491:A:99:ARG:NH1 1:A:147:GLN:OE1 2.46 0.491:B:422:ALA:HB1 1:B:494:TYR:HB3 1.94 0.491:C:804:LEU:HD22 1:C:927:LEU:HD11 1.94 0.491:A:609:ALA:HB1 1:A:614:GLN:HB2 1.93 0.491:B:334:PHE:HB2 1:B:388:VAL:HG23 1.94 0.491:B:389:VAL:HG11 1:B:397:ILE:HD11 1.95 0.491:A:1013:GLU:OE1 1:C:1022:VAL:N 2.46 0.491:C:886:TYR:HA 1:C:889:ASN:HD22 1.78 0.491:B:807:LYS:HD2 1:B:924:SER:HB2 1.95 0.48





Clashoverlap (Å)

1:A:878:ILE:HG13 1:C:694:ILE:HG12 1.95 0.481:B:591:SER:OG 1:B:592:SER:N 2.46 0.48

1:B:958:VAL:HG12 1:B:961:ASP:H 1.77 0.481:C:1073:ARG:NH1 1:C:1100:ASP:O 2.46 0.481:C:99:ARG:HE 1:C:170:LEU:HD23 1.77 0.481:B:871:GLY:HA3 1:B:1016:LEU:HB3 1.94 0.481:C:237:ALA:HB1 1:C:245:TRP:HB3 1.95 0.481:C:94:LYS:HB3 1:C:179:PHE:HA 1.95 0.481:B:25:VAL:HG13 1:B:76:PHE:HB3 1.96 0.481:C:25:VAL:HG22 1:C:76:PHE:HD2 1.79 0.481:A:445:HIS:H 1:A:460:PHE:HZ 1.61 0.48

1:A:808:VAL:HA 1:A:931:GLN:HE21 1.79 0.481:B:194:LEU:HB3 1:B:222:LEU:HB2 1.95 0.481:B:322:LEU:HA 1:B:349:VAL:H 1.78 0.481:B:582:SER:HB2 1:B:597:LEU:HB3 1.94 0.481:C:424:ASN:ND2 1:C:492:GLN:OE1 2.46 0.481:C:394:VAL:HG21 1:C:494:TYR:HD2 1.78 0.481:C:332:THR:O 1:C:495:ARG:NH1 2.47 0.481:A:1029:TYR:O 1:A:1049:TYR:N 2.44 0.481:C:586:PRO:HD3 1:C:674:ILE:HD11 1.96 0.481:A:48:ARG:HB2 1:A:266:TYR:CD2 2.49 0.471:C:422:ALA:HB1 1:C:494:TYR:HB3 1.95 0.471:C:848:THR:H 1:C:851:MET:HE3 1.79 0.47

1:C:429:ASP:OD2 1:C:495:ARG:NH2 2.47 0.471:A:804:LEU:HD13 1:A:1043:VAL:HG21 1.96 0.471:A:1070:TYR:HD2 1:A:1119:VAL:HG21 1.78 0.471:B:116:ILE:HG12 1:B:125:ILE:HG12 1.95 0.471:C:344:LYS:HA 1:C:383:TYR:HA 1.97 0.47

1:A:441:ARG:HH22 1:A:456:SER:HB3 1.80 0.471:C:182:LEU:HD22 1:C:203:ILE:HD12 1.96 0.471:C:196:VAL:HB 1:C:220:PHE:H 1.80 0.47

1:C:1062:ALA:HB3 1:C:1114:ILE:HG12 1.97 0.471:C:1111:VAL:HB 1:C:1114:ILE:HD11 1.97 0.471:C:804:LEU:HD21 1:C:920:LEU:HD13 1.95 0.471:B:331:ALA:HB3 1:B:334:PHE:HE1 1.79 0.471:C:126:ARG:HG2 1:C:162:GLU:HG3 1.97 0.471:A:1000:ILE:O 1:A:1004:ALA:N 2.47 0.46

1:A:708:VAL:HG23 1:A:929:LYS:HD2 1.97 0.461:C:102:VAL:HG23 1:C:115:ILE:HG12 1.97 0.461:A:175:LYS:HZ2 1:A:180:LYS:HD2 1.80 0.461:B:38:ARG:NH2 1:B:210:PRO:O 2.47 0.46





Clashoverlap (Å)

1:A:361:PHE:HA 1:A:423:TRP:HB2 1.97 0.461:A:711:VAL:HG22 1:A:1041:GLY:HA2 1.97 0.461:B:429:ASP:O 1:B:435:ASN:ND2 2.38 0.461:C:1062:ALA:O 1:C:1115:ILE:N 2.38 0.461:B:348:CYS:SG 1:B:349:VAL:N 2.89 0.461:C:712:SER:OG 1:C:713:MET:N 2.49 0.461:A:878:ILE:HG23 1:A:883:GLN:HE21 1.80 0.461:B:23:ASP:HB3 1:B:244:ILE:HG23 1.97 0.46

1:A:389:VAL:HG11 1:A:397:ILE:HD11 1.99 0.451:A:405:ILE:HD13 1:A:409:ASN:HD22 1.81 0.451:C:99:ARG:CZ 1:C:172:VAL:HG12 2.45 0.45

1:B:328:VAL:HG13 1:B:343:LYS:HD2 1.98 0.451:B:326:GLY:HA2 1:B:330:ASN:HB3 1.99 0.451:A:835:GLN:NE2 1:C:600:ASP:O 2.48 0.451:A:48:ARG:HB2 1:A:266:TYR:HD2 1.80 0.451:A:1018:GLN:NE2 1:A:1030:HIS:O 2.44 0.451:C:537:VAL:HB 1:C:574:SER:HB3 1.97 0.451:B:405:ILE:HG12 1:B:409:ASN:HD22 1.82 0.451:C:598:TYR:HB2 1:C:635:CYS:HB2 1.98 0.451:A:102:VAL:HB 1:A:232:ARG:HB3 1.99 0.451:A:365:LYS:NZ 1:A:366:CYS:O 2.49 0.451:B:188:LYS:HE3 1:B:195:TYR:HD2 1.82 0.45

1:A:363:THR:HG21 1:A:422:ALA:HB3 1.99 0.441:B:337:VAL:HG12 1:B:409:ASN:HB3 2.00 0.441:A:897:VAL:HA 1:A:900:GLU:HB2 1.99 0.44

1:A:109:ASN:HD22 1:A:131:GLU:HG2 1.82 0.441:A:585:THR:HB 1:A:594:VAL:HG12 1.98 0.441:C:425:THR:HB 1:C:428:ILE:HB 1.98 0.441:A:917:GLN:O 1:A:921:THR:OG1 2.27 0.44

1:C:871:GLY:HA2 1:C:1016:LEU:HD22 1.98 0.441:A:31:THR:O 1:A:68:GLY:N 2.42 0.44

1:B:114:VAL:HG11 1:B:224:LEU:HD13 1.98 0.441:A:582:SER:HB2 1:A:597:LEU:HB3 2.00 0.441:B:1057:PHE:HB3 1:B:1078:VAL:HG13 2.00 0.441:C:310:SER:N 1:C:524:CYS:O 2.50 0.441:A:591:SER:OG 1:A:592:SER:N 2.50 0.441:B:521:LYS:HD3 1:B:540:PRO:HD3 1.99 0.441:A:959:LEU:HD23 1:A:962:ILE:HD12 2.00 0.441:B:1063:ILE:HG23 1:B:1117:ASN:HB3 2.00 0.441:C:808:VAL:HG12 1:C:809:THR:HG23 2.00 0.441:B:352:TYR:HB3 1:B:355:LEU:HB2 1.99 0.43





Clashoverlap (Å)

1:C:766:GLN:NE2 1:C:1012:SER:OG 2.45 0.431:C:92:THR:N 1:C:251:ALA:O 2.47 0.43

1:A:745:LEU:HD22 1:A:990:VAL:HG21 2.00 0.431:A:81:ILE:HG21 1:A:254:VAL:HG21 1.98 0.431:A:98:VAL:O 1:A:183:ARG:NH2 2.46 0.43

1:C:1071:PHE:HZ 1:C:1111:VAL:HG21 1.83 0.431:C:564:ASP:OD2 1:C:567:THR:OG1 2.25 0.431:A:1108:CYS:SG 1:A:1109:ASP:N 2.91 0.431:A:451:PHE:HD2 1:B:192:GLY:HA3 1.82 0.431:C:685:SER:OG 1:C:686:SER:N 2.51 0.431:B:584:ILE:HB 1:B:595:ALA:HB3 1.99 0.431:C:1012:SER:HA 1:C:1016:LEU:HD12 2.01 0.431:C:390:LYS:HE2 1:C:481:TYR:HD1 1.83 0.431:A:444:ARG:NH1 1:A:454:ASP:OD2 2.52 0.431:A:238:PHE:H 1:A:247:THR:HA 1.83 0.43

1:B:324:PRO:HD2 1:B:345:ILE:HG23 2.01 0.431:A:1063:ILE:HG12 1:A:1117:ASN:HD22 1.83 0.43

1:B:31:THR:O 1:B:68:GLY:N 2.50 0.431:B:822:CYS:HB3 1:B:833:CYS:HB2 1.91 0.431:B:82:PRO:HB3 1:B:84:LYS:HE3 2.00 0.431:B:182:LEU:HB2 1:B:203:ILE:HD13 1.99 0.431:A:420:VAL:HG22 1:A:498:VAL:HG22 2.00 0.431:A:694:ILE:HG22 1:A:1059:THR:HB 2.01 0.431:B:179:PHE:HB2 1:B:205:VAL:HB 2.00 0.421:B:277:ASP:HB3 1:B:280:GLN:HG2 2.01 0.421:B:186:VAL:HG13 1:B:257:LEU:HD11 2.02 0.421:A:21:THR:HG22 1:A:135:ASN:H 1.84 0.421:A:152:ILE:HD13 1:A:234:ILE:HD13 2.02 0.421:A:96:ASN:O 1:A:99:ARG:NE 2.51 0.421:B:955:ILE:HB 1:B:974:GLN:HE22 1.83 0.42

1:C:704:ILE:HG12 1:C:1047:VAL:HG22 2.02 0.421:A:127:ALA:HB3 1:A:161:PHE:H 1.84 0.421:A:787:ILE:HD11 1:A:913:ILE:HD12 2.01 0.421:B:104:GLY:HA2 1:B:226:ILE:HD12 2.01 0.421:B:203:ILE:HB 1:B:205:VAL:HG23 2.01 0.42

1:B:282:PRO:HG3 1:B:619:TRP:CE2 2.55 0.421:B:758:ARG:O 1:B:762:GLU:N 2.45 0.42

1:C:1052:SER:OG 1:C:1053:GLN:N 2.52 0.421:B:248:SER:OG 1:B:249:ALA:N 2.52 0.421:A:209:LEU:HB2 1:A:253:PHE:CZ 2.55 0.421:B:1029:TYR:HB2 1:B:1049:TYR:HB3 2.00 0.42





Clashoverlap (Å)

1:B:286:LEU:HD11 1:B:300:TYR:HB2 2.01 0.421:B:429:ASP:OD2 1:B:495:ARG:NE 2.49 0.421:C:83:PHE:HE2 1:C:189:ASN:HB2 1.84 0.421:C:26:GLN:HB2 1:C:75:THR:HA 2.02 0.421:B:285:GLU:OE1 1:B:619:TRP:NE1 2.52 0.421:C:248:SER:OG 1:C:249:ALA:N 2.51 0.421:B:697:PRO:O 1:B:1092:PHE:N 2.53 0.421:C:329:PHE:HA 1:C:497:VAL:HG21 2.01 0.421:C:365:LYS:HB2 1:C:420:VAL:HB 2.02 0.421:B:1079:PHE:HB2 1:B:1084:TRP:CH2 2.54 0.421:B:923:THR:OG1 1:B:924:SER:N 2.51 0.421:A:407:ASP:OD2 1:A:447:LYS:NZ 2.39 0.411:B:197:TYR:CD1 1:B:218:PRO:HA 2.55 0.411:B:710:PRO:HA 1:B:1041:GLY:HA3 2.03 0.41

1:A:1054:GLU:HG2 1:B:876:LEU:HD21 2.01 0.411:C:887:ARG:NH1 1:C:1031:LEU:O 2.51 0.411:C:377:LEU:HB3 1:C:501:PHE:HZ 1.85 0.411:A:444:ARG:HH22 1:A:448:LEU:HG 1.84 0.411:B:631:THR:OG1 1:B:634:GLY:N 2.49 0.411:C:116:ILE:HG12 1:C:125:ILE:HG12 2.02 0.411:C:600:ASP:N 1:C:633:ALA:O 2.44 0.41

1:B:1080:ASN:HB3 1:B:1083:SER:H 1.86 0.411:C:1079:PHE:HB2 1:C:1084:TRP:CD2 2.55 0.411:A:83:PHE:CZ 1:A:86:GLY:HA2 2.56 0.411:A:305:PHE:HZ 1:A:601:VAL:HG11 1.85 0.411:A:96:ASN:HB2 1:A:99:ARG:HH21 1.86 0.411:C:545:PHE:HB2 1:C:563:ARG:HH21 1.86 0.411:B:663:VAL:H 1:B:672:LYS:N 2.19 0.41

1:C:182:LEU:HD23 1:C:201:GLN:HE21 1.86 0.411:C:546:GLN:H 1:C:549:GLN:HB2 1.86 0.411:A:39:GLY:HA3 1:A:60:LEU:HB3 2.02 0.411:B:1080:ASN:HB3 1:B:1082:THR:H 1.86 0.411:B:888:PHE:HE2 1:B:898:LEU:HD13 1.86 0.411:A:1071:PHE:HZ 1:A:1111:VAL:HG21 1.85 0.411:A:372:THR:HG21 1:B:968:PRO:HD3 2.02 0.411:C:99:ARG:HH21 1:C:170:LEU:HG 1.85 0.411:B:683:ALA:HB3 1:C:769:GLN:HG2 2.03 0.41

1:A:1111:VAL:HG13 1:B:899:TYR:HB3 2.02 0.411:A:735:LEU:HA 1:A:738:TYR:HD2 1.86 0.411:A:112:GLN:NE2 1:C:453:ARG:HH21 2.19 0.411:C:893:VAL:HA 1:C:1091:PHE:HE1 1.86 0.41





Clashoverlap (Å)

1:A:102:VAL:N 1:A:232:ARG:O 2.42 0.401:B:788:LEU:HD23 1:B:788:LEU:HA 1.82 0.401:C:363:THR:HG21 1:C:394:VAL:HG11 2.03 0.401:C:649:ASP:HB3 1:C:659:SER:HB2 2.03 0.401:C:313:VAL:HG11 1:C:519:LEU:HD12 2.03 0.401:B:76:PHE:CZ 1:B:235:LEU:HB2 2.56 0.40

1:A:306:ARG:NH2 1:B:727:ASP:OD1 2.43 0.401:B:632:GLN:HE21 1:C:825:ASP:HA 1.86 0.401:A:373:LYS:HE2 1:B:965:ARG:HG2 2.04 0.40

1:C:1059:THR:HG22 1:C:1078:VAL:HG12 2.02 0.401:C:21:THR:HB 1:C:135:ASN:HB2 2.04 0.401:C:25:VAL:HA 1:C:76:PHE:HB3 2.02 0.401:C:48:ARG:HB2 1:C:266:TYR:CD2 2.57 0.401:C:469:PRO:HA 1:C:471:ALA:H 1.87 0.401:A:530:ASN:H 1:A:565:PRO:HG2 1.87 0.401:B:405:ILE:O 1:B:410:TYR:N 2.40 0.40

1:C:1060:ALA:HA 1:C:1061:PRO:HD3 1.93 0.40

There are no symmetry-related clashes.

5.3 Torsion angles i○

5.3.1 Protein backbone i○

In the following table, the Percentiles column shows the percent Ramachandran outliers of thechain as a percentile score with respect to all PDB entries followed by that with respect to all EMentries.

The Analysed column shows the number of residues for which the backbone conformation wasanalysed, and the total number of residues.

Mol Chain Analysed Favoured Allowed Outliers Percentiles

1 A 1054/1215 (87%) 962 (91%) 92 (9%) 0 100 100

1 B 1054/1215 (87%) 973 (92%) 81 (8%) 0 100 100

1 C 1055/1215 (87%) 982 (93%) 73 (7%) 0 100 100

All All 3163/3645 (87%) 2917 (92%) 246 (8%) 0 100 100

There are no Ramachandran outliers to report.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#torsion_angles

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#protein_backbone


5.3.2 Protein sidechains i○

In the following table, the Percentiles column shows the percent sidechain outliers of the chainas a percentile score with respect to all PDB entries followed by that with respect to all EMentries.

The Analysed column shows the number of residues for which the sidechain conformation wasanalysed, and the total number of residues.

Mol Chain Analysed Rotameric Outliers Percentiles

1 A 926/1053 (88%) 926 (100%) 0 100 100

1 B 927/1053 (88%) 926 (100%) 1 (0%) 93 97

1 C 927/1053 (88%) 927 (100%) 0 100 100

All All 2780/3159 (88%) 2779 (100%) 1 (0%) 100 100

All (1) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 B 589 ASN

Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (17)such sidechains are listed below:

Mol Chain Res Type1 A 112 GLN1 A 230 ASN1 A 733 ASN1 A 883 GLN1 A 908 GLN1 A 931 GLN1 A 1117 ASN1 B 112 GLN1 B 733 ASN1 B 806 ASN1 B 883 GLN1 B 896 ASN1 C 112 GLN1 C 201 GLN1 C 347 ASN1 C 889 ASN1 C 908 GLN

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#protein_sidechains


5.3.3 RNA i○

There are no RNA molecules in this entry.

5.4 Non-standard residues in protein, DNA, RNA chains i○

There are no non-standard protein/DNA/RNA residues in this entry.

5.5 Carbohydrates i○

51 monosaccharides are modelled in this entry.

In the following table, the Counts columns list the number of bonds (or angles) for which Mogulstatistics could be retrieved, the number of bonds (or angles) that are observed in the model andthe number of bonds (or angles) that are defined in the Chemical Component Dictionary. TheLink column lists molecule types, if any, to which the group is linked. The Z score for a bondlength (or angle) is the number of standard deviations the observed value is removed from theexpected value. A bond length (or angle) with |Z| > 2 is considered an outlier worth inspection.RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles).

Mol Type Chain Res Link Bond lengths Bond anglesCounts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2

2 NAG D 1 1,2 14,14,15 0.40 0 17,19,21 0.59 02 NAG D 2 2 14,14,15 0.30 0 17,19,21 1.08 1 (5%)2 BMA D 3 2 11,11,12 0.94 0 15,15,17 0.80 03 NAG E 1 1,3 14,14,15 0.40 0 17,19,21 0.63 03 NAG E 2 3 14,14,15 0.29 0 17,19,21 0.49 03 BMA E 3 3 11,11,12 0.63 0 15,15,17 0.89 03 MAN E 4 3 11,11,12 0.81 0 15,15,17 1.07 2 (13%)2 NAG F 1 1,2 14,14,15 0.54 0 17,19,21 0.65 02 NAG F 2 2 14,14,15 0.37 0 17,19,21 0.46 02 BMA F 3 2 11,11,12 0.66 0 15,15,17 1.01 1 (6%)4 NAG G 1 1,4 14,14,15 0.45 0 17,19,21 0.56 04 NAG G 2 4 14,14,15 0.22 0 17,19,21 0.51 04 NAG H 1 1,4 14,14,15 0.41 0 17,19,21 0.64 04 NAG H 2 4 14,14,15 0.26 0 17,19,21 0.56 04 NAG I 1 1,4 14,14,15 0.72 1 (7%) 17,19,21 0.63 04 NAG I 2 4 14,14,15 0.46 0 17,19,21 0.48 02 NAG J 1 1,2 14,14,15 0.30 0 17,19,21 0.45 02 NAG J 2 2 14,14,15 0.30 0 17,19,21 0.49 02 BMA J 3 2 11,11,12 0.88 0 15,15,17 0.82 02 NAG K 1 1,2 14,14,15 0.35 0 17,19,21 0.62 1 (5%)2 NAG K 2 2 14,14,15 0.31 0 17,19,21 0.50 0

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#rna

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#nonstandard_residues_and_ligands




2 BMA K 3 2 11,11,12 0.82 0 15,15,17 0.80 04 NAG L 1 1,4 14,14,15 0.29 0 17,19,21 0.37 04 NAG L 2 4 14,14,15 0.22 0 17,19,21 0.64 1 (5%)2 NAG M 1 1,2 14,14,15 0.30 0 17,19,21 0.56 02 NAG M 2 2 14,14,15 0.43 0 17,19,21 0.63 02 BMA M 3 2 11,11,12 0.77 0 15,15,17 0.85 02 NAG N 1 1,2 14,14,15 0.36 0 17,19,21 0.53 02 NAG N 2 2 14,14,15 0.22 0 17,19,21 0.69 1 (5%)2 BMA N 3 2 11,11,12 0.86 0 15,15,17 0.78 04 NAG O 1 1,4 14,14,15 0.41 0 17,19,21 0.78 1 (5%)4 NAG O 2 4 14,14,15 0.60 0 17,19,21 0.38 04 NAG P 1 1,4 14,14,15 0.28 0 17,19,21 0.49 04 NAG P 2 4 14,14,15 0.29 0 17,19,21 0.42 04 NAG Q 1 1,4 14,14,15 0.31 0 17,19,21 0.50 04 NAG Q 2 4 14,14,15 0.34 0 17,19,21 0.42 02 NAG R 1 1,2 14,14,15 0.21 0 17,19,21 0.98 1 (5%)2 NAG R 2 2 14,14,15 0.20 0 17,19,21 0.58 02 BMA R 3 2 11,11,12 0.74 0 15,15,17 0.95 1 (6%)5 NAG S 1 1,5 14,14,15 0.36 0 17,19,21 0.42 05 NAG S 2 5 14,14,15 0.26 0 17,19,21 0.55 05 BMA S 3 5 11,11,12 0.85 0 15,15,17 1.36 1 (6%)5 MAN S 4 5 11,11,12 1.01 1 (9%) 15,15,17 1.30 2 (13%)2 NAG T 1 1,2 14,14,15 0.63 1 (7%) 17,19,21 0.59 02 NAG T 2 2 14,14,15 0.31 0 17,19,21 0.70 02 BMA T 3 2 11,11,12 0.65 0 15,15,17 1.05 1 (6%)2 NAG U 1 1,2 14,14,15 0.45 0 17,19,21 0.46 02 NAG U 2 2 14,14,15 0.34 0 17,19,21 0.62 1 (5%)2 BMA U 3 2 11,11,12 0.76 0 15,15,17 0.85 04 NAG V 1 1,4 14,14,15 0.26 0 17,19,21 0.39 04 NAG V 2 4 14,14,15 0.26 0 17,19,21 0.50 0

In the following table, the Chirals column lists the number of chiral outliers, the number of chiralcenters analysed, the number of these observed in the model and the number defined in theChemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns.’-’ means no outliers of that kind were identified.

Mol Type Chain Res Link Chirals Torsions Rings2 NAG D 1 1,2 - 2/6/23/26 0/1/1/12 NAG D 2 2 - 2/6/23/26 0/1/1/12 BMA D 3 2 - 0/2/19/22 0/1/1/1



Continued from previous page...Mol Type Chain Res Link Chirals Torsions Rings3 NAG E 1 1,3 - 2/6/23/26 0/1/1/13 NAG E 2 3 - 1/6/23/26 0/1/1/13 BMA E 3 3 - 2/2/19/22 0/1/1/13 MAN E 4 3 - 2/2/19/22 0/1/1/12 NAG F 1 1,2 - 2/6/23/26 0/1/1/12 NAG F 2 2 - 2/6/23/26 0/1/1/12 BMA F 3 2 - 0/2/19/22 0/1/1/14 NAG G 1 1,4 - 2/6/23/26 0/1/1/14 NAG G 2 4 - 2/6/23/26 0/1/1/14 NAG H 1 1,4 - 0/6/23/26 0/1/1/14 NAG H 2 4 - 0/6/23/26 0/1/1/14 NAG I 1 1,4 - 1/6/23/26 0/1/1/14 NAG I 2 4 - 2/6/23/26 0/1/1/12 NAG J 1 1,2 - 1/6/23/26 0/1/1/12 NAG J 2 2 - 0/6/23/26 0/1/1/12 BMA J 3 2 - 2/2/19/22 0/1/1/12 NAG K 1 1,2 - 0/6/23/26 0/1/1/12 NAG K 2 2 - 2/6/23/26 0/1/1/12 BMA K 3 2 - 2/2/19/22 0/1/1/14 NAG L 1 1,4 - 1/6/23/26 0/1/1/14 NAG L 2 4 - 2/6/23/26 0/1/1/12 NAG M 1 1,2 - 2/6/23/26 0/1/1/12 NAG M 2 2 - 2/6/23/26 0/1/1/12 BMA M 3 2 - 2/2/19/22 0/1/1/12 NAG N 1 1,2 - 2/6/23/26 0/1/1/12 NAG N 2 2 - 0/6/23/26 0/1/1/12 BMA N 3 2 - 2/2/19/22 0/1/1/14 NAG O 1 1,4 - 2/6/23/26 0/1/1/14 NAG O 2 4 - 0/6/23/26 0/1/1/14 NAG P 1 1,4 - 2/6/23/26 0/1/1/14 NAG P 2 4 - 2/6/23/26 0/1/1/14 NAG Q 1 1,4 - 2/6/23/26 0/1/1/14 NAG Q 2 4 - 2/6/23/26 0/1/1/12 NAG R 1 1,2 - 1/6/23/26 0/1/1/12 NAG R 2 2 - 2/6/23/26 0/1/1/12 BMA R 3 2 - 2/2/19/22 0/1/1/1



Continued from previous page...Mol Type Chain Res Link Chirals Torsions Rings5 NAG S 1 1,5 - 2/6/23/26 0/1/1/15 NAG S 2 5 - 2/6/23/26 0/1/1/15 BMA S 3 5 - 1/2/19/22 0/1/1/15 MAN S 4 5 - 0/2/19/22 0/1/1/12 NAG T 1 1,2 - 0/6/23/26 0/1/1/12 NAG T 2 2 - 2/6/23/26 0/1/1/12 BMA T 3 2 - 2/2/19/22 0/1/1/12 NAG U 1 1,2 - 0/6/23/26 0/1/1/12 NAG U 2 2 - 1/6/23/26 0/1/1/12 BMA U 3 2 - 0/2/19/22 0/1/1/14 NAG V 1 1,4 - 2/6/23/26 0/1/1/14 NAG V 2 4 - 0/6/23/26 0/1/1/1

All (3) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)5 S 4 MAN C1-C2 2.63 1.58 1.522 T 1 NAG O5-C1 -2.08 1.40 1.434 I 1 NAG O5-C1 2.06 1.47 1.43


Mol Chain Res Type Atoms Z Observed(o) Ideal(o)5 S 3 BMA C1-O5-C5 3.79 117.33 112.192 D 2 NAG C1-O5-C5 3.50 116.94 112.192 R 1 NAG C1-O5-C5 3.22 116.55 112.195 S 4 MAN C1-O5-C5 2.94 116.17 112.192 F 3 BMA C1-O5-C5 2.85 116.06 112.193 E 4 MAN C1-O5-C5 2.53 115.62 112.194 O 1 NAG C1-O5-C5 2.51 115.59 112.192 T 3 BMA C1-O5-C5 2.47 115.54 112.192 R 3 BMA C1-O5-C5 2.45 115.51 112.192 N 2 NAG C1-O5-C5 2.39 115.43 112.194 L 2 NAG C1-O5-C5 2.31 115.33 112.195 S 4 MAN O2-C2-C3 -2.18 105.78 110.143 E 4 MAN O2-C2-C3 -2.16 105.81 110.142 U 2 NAG C1-O5-C5 2.08 115.02 112.192 K 1 NAG C1-O5-C5 2.01 114.92 112.19



All (69) torsion outliers are listed below:

Mol Chain Res Type Atoms2 K 2 NAG O5-C5-C6-O62 N 3 BMA C4-C5-C6-O62 D 1 NAG O5-C5-C6-O64 O 1 NAG O5-C5-C6-O62 K 3 BMA O5-C5-C6-O64 P 2 NAG O5-C5-C6-O63 E 1 NAG O5-C5-C6-O64 O 1 NAG C4-C5-C6-O62 N 3 BMA O5-C5-C6-O62 R 3 BMA O5-C5-C6-O64 L 2 NAG O5-C5-C6-O64 G 1 NAG O5-C5-C6-O62 M 1 NAG O5-C5-C6-O62 T 2 NAG O5-C5-C6-O62 K 2 NAG C4-C5-C6-O62 N 1 NAG C4-C5-C6-O65 S 1 NAG O5-C5-C6-O62 N 1 NAG O5-C5-C6-O62 F 1 NAG O5-C5-C6-O62 D 1 NAG C4-C5-C6-O62 T 3 BMA O5-C5-C6-O62 F 2 NAG C4-C5-C6-O62 K 3 BMA C4-C5-C6-O64 P 2 NAG C4-C5-C6-O62 T 2 NAG C4-C5-C6-O65 S 1 NAG C4-C5-C6-O62 F 1 NAG C4-C5-C6-O63 E 1 NAG C4-C5-C6-O62 R 2 NAG O5-C5-C6-O65 S 2 NAG O5-C5-C6-O64 I 2 NAG O5-C5-C6-O62 M 1 NAG C4-C5-C6-O62 J 3 BMA C4-C5-C6-O62 R 3 BMA C4-C5-C6-O63 E 4 MAN O5-C5-C6-O64 G 2 NAG O5-C5-C6-O62 D 2 NAG O5-C5-C6-O64 L 2 NAG C4-C5-C6-O62 R 2 NAG C4-C5-C6-O62 M 3 BMA O5-C5-C6-O64 P 1 NAG O5-C5-C6-O64 G 2 NAG C4-C5-C6-O6



Continued from previous page...Mol Chain Res Type Atoms3 E 4 MAN C4-C5-C6-O62 D 2 NAG C4-C5-C6-O62 F 2 NAG O5-C5-C6-O64 Q 1 NAG C4-C5-C6-O64 G 1 NAG C4-C5-C6-O63 E 3 BMA O5-C5-C6-O65 S 2 NAG C4-C5-C6-O64 I 1 NAG O5-C5-C6-O64 I 2 NAG C4-C5-C6-O62 J 3 BMA O5-C5-C6-O63 E 3 BMA C4-C5-C6-O64 V 1 NAG C4-C5-C6-O62 R 1 NAG O5-C5-C6-O62 U 2 NAG O5-C5-C6-O62 M 2 NAG C4-C5-C6-O64 Q 1 NAG O5-C5-C6-O62 M 3 BMA C4-C5-C6-O62 M 2 NAG O5-C5-C6-O64 L 1 NAG O5-C5-C6-O64 V 1 NAG O5-C5-C6-O64 Q 2 NAG C4-C5-C6-O64 Q 2 NAG O5-C5-C6-O65 S 3 BMA O5-C5-C6-O62 J 1 NAG C4-C5-C6-O62 T 3 BMA C4-C5-C6-O63 E 2 NAG O5-C5-C6-O64 P 1 NAG C4-C5-C6-O6

There are no ring outliers.

1 monomer is involved in 1 short contact:

Mol Chain Res Type Clashes Symm-Clashes4 G 1 NAG 1 0

The following is a two-dimensional graphical depiction of Mogul quality analysis of bond lengths,bond angles, torsion angles, and ring geometry for oligosaccharide.


Oligosaccharide Chain D

Bond lengths Bond angles

Torsions Rings

Oligosaccharide Chain F


Torsions Rings


Oligosaccharide Chain J


Torsions Rings

Oligosaccharide Chain K


Torsions Rings


Oligosaccharide Chain M


Torsions Rings

Oligosaccharide Chain N


Torsions Rings


Oligosaccharide Chain R


Torsions Rings

Oligosaccharide Chain T


Torsions Rings


Oligosaccharide Chain U


Torsions Rings

Oligosaccharide Chain E


Torsions Rings


Oligosaccharide Chain G


Torsions Rings


Oligosaccharide Chain H


Torsions Rings


Oligosaccharide Chain I


Torsions Rings


Oligosaccharide Chain L


Torsions Rings


Oligosaccharide Chain O


Torsions Rings


Oligosaccharide Chain P


Torsions Rings


Oligosaccharide Chain Q


Torsions Rings


Oligosaccharide Chain V


Torsions Rings


Oligosaccharide Chain S


Torsions Rings

5.6 Ligand geometry i○

15 ligands are modelled in this entry.

In the following table, the Counts columns list the number of bonds (or angles) for which Mogulstatistics could be retrieved, the number of bonds (or angles) that are observed in the model andthe number of bonds (or angles) that are defined in the Chemical Component Dictionary. TheLink column lists molecule types, if any, to which the group is linked. The Z score for a bondlength (or angle) is the number of standard deviations the observed value is removed from theexpected value. A bond length (or angle) with |Z| > 2 is considered an outlier worth inspection.RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles).


6 NAG A 1310 1 14,14,15 0.22 0 17,19,21 0.63 1 (5%)6 NAG C 1304 1 14,14,15 0.45 0 17,19,21 0.71 1 (5%)6 NAG C 1308 1 14,14,15 0.26 0 17,19,21 0.65 1 (5%)6 NAG A 1301 1 14,14,15 0.39 0 17,19,21 0.73 1 (5%)6 NAG B 1321 1 14,14,15 0.26 0 17,19,21 0.43 06 NAG A 1305 1 14,14,15 0.42 0 17,19,21 0.52 06 NAG A 1316 1 14,14,15 0.45 0 17,19,21 0.66 1 (5%)6 NAG B 1311 1 14,14,15 0.40 0 17,19,21 0.41 0




6 NAG C 1320 1 14,14,15 0.45 0 17,19,21 0.61 1 (5%)6 NAG B 1308 1 14,14,15 0.31 0 17,19,21 0.47 06 NAG C 1301 1 14,14,15 0.36 0 17,19,21 0.62 1 (5%)6 NAG B 1320 1 14,14,15 0.27 0 17,19,21 0.64 1 (5%)6 NAG B 1301 1 14,14,15 0.28 0 17,19,21 0.40 06 NAG C 1312 1 14,14,15 0.34 0 17,19,21 0.55 06 NAG C 1307 1 14,14,15 0.31 0 17,19,21 0.32 0

In the following table, the Chirals column lists the number of chiral outliers, the number of chiralcenters analysed, the number of these observed in the model and the number defined in theChemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns.’-’ means no outliers of that kind were identified.

Mol Type Chain Res Link Chirals Torsions Rings6 NAG A 1310 1 - 2/6/23/26 0/1/1/16 NAG C 1304 1 - 0/6/23/26 0/1/1/16 NAG C 1308 1 - 2/6/23/26 0/1/1/16 NAG A 1301 1 - 2/6/23/26 0/1/1/16 NAG B 1321 1 - 0/6/23/26 0/1/1/16 NAG A 1305 1 - 2/6/23/26 0/1/1/16 NAG A 1316 1 - 2/6/23/26 0/1/1/16 NAG B 1311 1 - 2/6/23/26 0/1/1/16 NAG C 1320 1 - 0/6/23/26 0/1/1/16 NAG B 1308 1 - 1/6/23/26 0/1/1/16 NAG C 1301 1 - 2/6/23/26 0/1/1/16 NAG B 1320 1 - 2/6/23/26 0/1/1/16 NAG B 1301 1 - 2/6/23/26 0/1/1/16 NAG C 1312 1 - 0/6/23/26 0/1/1/16 NAG C 1307 1 - 1/6/23/26 0/1/1/1

There are no bond length outliers.


Mol Chain Res Type Atoms Z Observed(o) Ideal(o)6 A 1301 NAG C1-O5-C5 2.55 115.65 112.196 C 1304 NAG C1-O5-C5 2.55 115.65 112.196 B 1320 NAG C1-O5-C5 2.35 115.37 112.196 A 1316 NAG C1-O5-C5 2.32 115.34 112.196 C 1308 NAG C1-O5-C5 2.29 115.30 112.19



Continued from previous page...Mol Chain Res Type Atoms Z Observed(o) Ideal(o)6 A 1310 NAG C1-O5-C5 2.15 115.11 112.196 C 1301 NAG C1-O5-C5 2.12 115.06 112.196 C 1320 NAG C1-O5-C5 2.09 115.03 112.19


All (20) torsion outliers are listed below:

Mol Chain Res Type Atoms6 A 1316 NAG O5-C5-C6-O66 A 1301 NAG O5-C5-C6-O66 B 1320 NAG O5-C5-C6-O66 A 1316 NAG C4-C5-C6-O66 A 1305 NAG O5-C5-C6-O66 A 1301 NAG C4-C5-C6-O66 B 1311 NAG C4-C5-C6-O66 B 1301 NAG O5-C5-C6-O66 B 1311 NAG O5-C5-C6-O66 A 1310 NAG O5-C5-C6-O66 B 1320 NAG C4-C5-C6-O66 B 1301 NAG C4-C5-C6-O66 A 1310 NAG C4-C5-C6-O66 C 1308 NAG O5-C5-C6-O66 C 1301 NAG O5-C5-C6-O66 C 1308 NAG C4-C5-C6-O66 C 1301 NAG C4-C5-C6-O66 B 1308 NAG O5-C5-C6-O66 A 1305 NAG C4-C5-C6-O66 C 1307 NAG O5-C5-C6-O6

There are no ring outliers.

2 monomers are involved in 2 short contacts:

Mol Chain Res Type Clashes Symm-Clashes6 A 1310 NAG 1 06 B 1301 NAG 1 0

5.7 Other polymers i○

There are no such residues in this entry.



5.8 Polymer linkage issues i○

There are no chain breaks in this entry.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#polymer_linkage


6 Map visualisation i○

This section contains visualisations of the EMDB entry EMD-7577. These allow visual inspectionof the internal detail of the map and identification of artifacts.

Images derived from a raw map, generated by summing the deposited half-maps, are presentedbelow the corresponding image components of the primary map to allow further visual inspectionand comparison with those of the primary map.

6.1 Orthogonal projections i○

6.1.1 Primary map

X Y Z

6.1.2 Raw map

X Y Z

The images above show the map projected in three orthogonal directions.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_visualisation

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#orthogonal_projections


6.2 Central slices i○

6.2.1 Primary map

X Index: 160 Y Index: 160 Z Index: 160

6.2.2 Raw map


The images above show central slices of the map in three orthogonal directions.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#central_slices


6.3 Largest variance slices i○

6.3.1 Primary map


6.3.2 Raw map


The images above show the largest variance slices of the map in three orthogonal directions.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#largest_variance_slices


6.4 Orthogonal surface views i○

6.4.1 Primary map

X Y Z

The images above show the 3D surface view of the map at the recommended contour level 0.069.These images, in conjunction with the slice images, may facilitate assessment of whether an ap-propriate contour level has been provided.

6.4.2 Raw map

X Y Z

These images show the 3D surface of the raw map. The raw map’s contour level was selected sothat its surface encloses the same volume as the primary map does at its recommended contourlevel.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#orthogonal_views


6.5 Mask visualisation i○

This section shows the 3D surface view of the primary map at 50% transparency overlaid with thespecified mask at 0% transparency

A mask typically either:

• Encompasses the whole structure

• Separates out a domain, a functional unit, a monomer or an area of interest from a largerstructure

6.5.1 emd_7577_msk_1.map i○

X Y Z

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#masks

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#masks


7 Map analysis i○

This section contains the results of statistical analysis of the map.

7.1 Map-value distribution i○

The map-value distribution is plotted in 128 intervals along the x-axis. The y-axis is logarithmic.A spike in this graph at zero usually indicates that the volume has been masked.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_analysis

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_value_distribution


7.2 Volume estimate i○

The volume at the recommended contour level is 76 nm3; this corresponds to an approximate massof 69 kDa.

The volume estimate graph shows how the enclosed volume varies with the contour level. Therecommended contour level is shown as a vertical line and the intersection between the line andthe curve gives the volume of the enclosed surface at the given level.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#volume_estimate


7.3 Rotationally averaged power spectrum i○

*Reported resolution corresponds to spatial frequency of 0.303 Å−1

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#raps


8 Fourier-Shell correlation i○

Fourier-Shell Correlation (FSC) is the most commonly used method to estimate the resolution ofsingle-particle and subtomogram-averaged maps. The shape of the curve depends on the imposedsymmetry, mask and whether or not the two 3D reconstructions used were processed from acommon reference. The reported resolution is shown as a black line. A curve is displayed for thehalf-bit criterion in addition to lines showing the 0.143 gold standard cut-off and 0.5 cut-off.

8.1 FSC i○

*Reported resolution corresponds to spatial frequency of 0.303 Å−1

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#fsc_validation

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#fsc_validation


8.2 Resolution estimates i○

Resolution estimate (Å) Estimation criterion (FSC cut-off)0.143 0.5 Half-bit

Reported by author 3.30 - -Author-provided FSC curve 3.36 3.74 3.38

Calculated* 3.72 4.24 3.80

*Resolution estimate based on FSC curve calculated by comparison of deposited half-maps. Thevalue from deposited half-maps intersecting FSC 0.143 CUT-OFF 3.72 differs from the reportedvalue 3.3 by more than 10 %

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#resolution_estimates


9 Map-model fit i○

This section contains information regarding the fit between EMDB map EMD-7577 and PDBmodel 6CRZ. Per-residue inclusion information can be found in section 3 on page 9.

9.1 Map-model overlay i○

X Y Z

The images above show the 3D surface view of the map at the recommended contour level 0.069at 50% transparency in yellow overlaid with a ribbon representation of the model coloured in blue.These images allow for the visual assessment of the quality of fit between the atomic model andthe map.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_model_fit

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_model_overlay


9.2 Atom inclusion i○

At the recommended contour level, 20% of all backbone atoms, 15% of all non-hydrogen atoms,are inside the map.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#atom_inclusion_by_contour

Full wwPDB EM Validation Report i - PDBj top page

Documents

Transcript of Full wwPDB EM Validation Report i - PDBj top page