Full wwPDB/EMDataBank EM Map/Model Validation Report · 2019. 7. 26. · Full wwPDB/EMDataBank EM...

Full wwPDB EM Map/Model Validation Report i○

Sep 24, 2020 – 10:10 PM EDT

PDB ID : 6NP0EMDB ID : EMD-0469

Title : Cryo-EM structure of 5HT3A receptor in presence of granisetronAuthors : Basak, S.; Chakrapani, S.

Deposited on : 2019-01-17Resolution : 2.92 Å(reported)

This is a Full wwPDB EM Map/Model 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.dev33Mogul : 1.8.5 (274361), CSD as541be (2020)

MolProbity : 4.02b-467buster-report : 1.1.7 (2018)

Percentile 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) : 2.14.6

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



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

Full wwPDB EM Map/Model Validation Report EMD-0469, 6NP0

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 2.92 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 theirfit to the map. The red, orange, yellow and green segments on the bar indicate the fraction ofresidues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria respectively. Agrey segment 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 489

1 B 489

1 C 489

1 D 489

1 E 489

2 F 3

2 H 3

2 J 3Continued on next page...

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


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

2 L 3

2 N 3

3 G 2

3 I 2

3 K 2

3 M 2

3 O 2


2 Entry composition i○

There are 6 unique types of molecules in this entry. The entry contains 16891 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 5-hydroxytryptamine receptor 3A.

Mol Chain Residues Atoms AltConf Trace

1 A 395 Total C N O S3260 2147 534 569 10 0 0

1 B 395 Total C N O S3260 2147 534 569 10 0 0

1 C 395 Total C N O S3260 2147 534 569 10 0 0

1 D 395 Total C N O S3260 2147 534 569 10 0 0

1 E 395 Total C N O S3260 2147 534 569 10 0 0

• 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 F 3 Total C N O39 22 2 15 0 0

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

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

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

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

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

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



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

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

3 K 2 Total C N O28 16 2 10 0 0

3 M 2 Total C N O28 16 2 10 0 0

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

• Molecule 4 is 2-acetamido-2-deoxy-beta-D-glucopyranose (three-letter code: NAG) (formula:C8H15NO6).

Mol Chain Residues Atoms AltConf

4 A 1 Total C N O28 16 2 10 0

4 A 1 Total C N O28 16 2 10 0

4 B 1 Total C N O28 16 2 10 0

4 B 1 Total C N O28 16 2 10 0

Continued on next page...


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

4 C 1 Total C N O28 16 2 10 0

4 C 1 Total C N O28 16 2 10 0

4 D 1 Total C N O28 16 2 10 0

4 D 1 Total C N O28 16 2 10 0

4 E 1 Total C N O28 16 2 10 0

4 E 1 Total C N O28 16 2 10 0

• Molecule 5 is 1-methyl-N-[(1R,5S)-9-methyl-9-azabicyclo[3.3.1]nonan-3-yl]indazole-3-carboxamide (three-letter code: CWB) (formula: C18H24N4O).


5 A 1 Total C N O23 18 4 1 0

5 B 1 Total C N O23 18 4 1 0

5 C 1 Total C N O23 18 4 1 0

5 D 1 Total C N O46 36 8 2 0

5 D 1 Total C N O46 36 8 2 0


• Molecule 6 is CHLORIDE ION (three-letter code: CL) (formula: Cl).


6 A 1 Total Cl1 1 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: 5-hydroxytryptamine receptor 3A

Chain A:

MET

ARG

LEU

CYS

ILE

PRO

GLN

VAL

LEU

LEU

ALA

LEU

PHE

LEU

SER

MET

LEU

THR

ALA

PRO

GLY

GLU

GLY

SER

ARG

ARG

ARG

ALA

THR

GLN

ALA

ARG

ASP

T7�

T8�

Q9�

L12

L13

L19

Y23

V27

R28

V39

S40

I41

E53

W68

D79

D91

S92

I93

D105

K108

Y116

P128

V132

C135

S136

N141

D145

F153

H158

T159

I160

Q161

D162

I163

N164

S170

P171

E172

V192

I203

�

A208

V214

I215

R218

F222

L227

L234

L258

Y262

D271

�T2

72�

L273

T276

�A2

77I2

78�

G279

�

L298

D312

R315

W320

L321

R322

�H3

23�

L326

�

A330

�W3

31�

I332

�L3

33C3

34�

L335

�GL

YGL

UGL

NPR

OME

TAL

AHI

SAR

GPR

OPR

OAL

ATH

RPH

EGL

NAL

AAS

NLY

STH

RAS

PAS

PCY

SSE

RGL

YSE

RAS

PLE

ULE

UPR

OAL

AME

TGL

YAS

NHI

SCY

SSE

RHI

SVA

LGL

YGL

Y

PRO

GLN

ASP

LEU

GLU

LYS

THR

PRO

ARG

GLY

ARG

GLY

SER

PRO

LEU

PRO

PRO

PRO

ARG

GLU

ALA

SER

L397

�A3

98�

V399

R400

�

R416

�

R420

R424

Y461

�S4

62�


Chain B:

MET

ARG

LEU

CYS

ILE

PRO

GLN

VAL

LEU

LEU

ALA

LEU

PHE

LEU

SER

MET

LEU

THR

ALA

PRO

GLY

GLU

GLY

SER

ARG

ARG

ARG

ALA

THR

GLN

ALA

ARG

ASP

T7�

T8�

Q9�

L12

L19

Y23

V27

R28

V39

S40

I41

E53

W68

D79

D91

S92

I93

D105

Y116

V132

C135

S136

N141

D145

F153

W156

L157

H158

T159

I160

Q161

D162

I163

N164

S170

P171

E172

G185

�

I203

�

A208

I215

R218

L227

L234

L244

G249

�

L258

Y262

D271

�T2

72�

L273

T276

�A2

77I2

78�

G279

�

L298

D312

R315

W320

L321

R322

�H3

23�

A330

�W3

31�

I332

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L335

�GL

YGL

UGL

NPR

OME

TAL

AHI

SAR

GPR

OPR

OAL

ATH

RPH

EGL

NAL

AAS

NLY

STH

RAS

PAS

PCY

SSE

RGL

YSE

RAS

PLE

ULE

UPR

OAL

AME

TGL

YAS

NHI

SCY

SSE

RHI

SVA

LGL

YGL

YPR

OGL

NAS

PLE

UGL

U

LYS

THR

PRO

ARG

GLY

ARG

GLY

SER

PRO

LEU

PRO

PRO

PRO

ARG

GLU

ALA

SER

L397

�A3

98�

V399

R400

�

Q404

�

R416

�

Y431

L452

�

Y461

�S4

62�


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


Chain C:ME

TAR

GLE

UCY

SIL

EPR

OGL

NVA

LLE

ULE

UAL

ALE

UPH

ELE

USE

RME

TLE

UTH

RAL

APR

OGL

YGL

UGL

YSE

RAR

GAR

GAR

GAL

ATH

RGL

NAL

AAR

GAS

PT7

�T8

�Q9

�

L12

L13

L19

N22

�Y2

3

R28

V39

S40

I41

E53

W68

D79

F80

D81

D91

S92

I93

D105

Y116

V132

C135

S136

N141

D145

F153

H158

T159

I160

Q161

D162

I163

N164

S170

P171

E172

G185

�

V192

A208

V214

I215

R218

L227

L234

G249

�

V252

L258

Y262

D271

�T2

72�

L273

T276

�A2

77I2

78�

G279

�

L298

Q311

�D3

12L3

13Q3

14�

R315

W320

L321

R322

�H3

23�

L326

�

A330

�W3

31�

I332

�L3

33C3

34�

L335

�GL

YGL

UGL

NPR

OME

TAL

AHI

SAR

GPR

OPR

OAL

ATH

RPH

EGL

NAL

AAS

NLY

STH

RAS

PAS

PCY

SSE

RGL

YSE

RAS

PLE

ULE

UPR

OAL

AME

TGL

YAS

NHI

SCY

SSE

RHI

SVA

L

GLY

GLY

PRO

GLN

ASP

LEU

GLU

LYS

THR

PRO

ARG

GLY

ARG

GLY

SER

PRO

LEU

PRO

PRO

PRO

ARG

GLU

ALA

SER

L397

�A3

98�

V399

R400

�

Q404

�

R416

�

R420

�

Y461

�S4

62�


Chain D:

MET

ARG

LEU

CYS

ILE

PRO

GLN

VAL

LEU

LEU

ALA

LEU

PHE

LEU

SER

MET

LEU

THR

ALA

PRO

GLY

GLU

GLY

SER

ARG

ARG

ARG

ALA

THR

GLN

ALA

ARG

ASP

T7�

T8�

Q9�

L12

L19

Y23

V27

R28

W33

V39

S40

I41

E53

W68

D79

D91

S92

I93

D105

P128

V132

C135

S136

N141

D145

F153

H158

T159

I160

Q161

D162

I163

N164

S170

P171

E172

V192

I203

�

A208

V214

I215

R218

F222

L227

I232

�F2

33L2

34

L258

Y262

D271

�T2

72�

L273

T276

�A2

77I2

78�

G279

�

L298

D312

R315

W320

L321

R322

�H3

23�

L326

�

A330

�W3

31�

I332

�

L335

�GL

YGL

UGL

NPR

OME

TAL

AHI

SAR

GPR

OPR

OAL

ATH

RPH

EGL

NAL

AAS

NLY

STH

RAS

PAS

PCY

SSE

RGL

YSE

RAS

PLE

ULE

UPR

OAL

AME

TGL

YAS

NHI

SCY

SSE

RHI

SVA

LGL

YGL

YPR

OGL

N

ASP

LEU

GLU

LYS

THR

PRO

ARG

GLY

ARG

GLY

SER

PRO

LEU

PRO

PRO

PRO

ARG

GLU

ALA

SER

L397

�A3

98�

V399

R400

�

Q404

�

R416

�

R424

L452

�

Y461

�S4

62�


Chain E:

MET

ARG

LEU

CYS

ILE

PRO

GLN

VAL

LEU

LEU

ALA

LEU

PHE

LEU

SER

MET

LEU

THR

ALA

PRO

GLY

GLU

GLY

SER

ARG

ARG

ARG

ALA

THR

GLN

ALA

ARG

ASP

T7�

T8�

Q9�

L12

L13

L19

Y23

R28

V39

S40

I41

E53

W68

D79

D91

S92

I93

D105

Y116

V132

C135

S136

N141

F153

W156

L157

H158

T159

I160

Q161

D162

I163

N164

S170

P171

E172

V192

I203

�

A208

V214

I215

R218

F222

L227

L234

L258

Y262

D271

�T2

72�

L273

T276

�A2

77I2

78�

G279

�

L298

D312

R315

W320

L321

R322

�H3

23�

A330

�W3

31�

I332

�L3

33C3

34�

L335

�GL

YGL

UGL

NPR

OME

TAL

AHI

SAR

GPR

OPR

OAL

ATH

RPH

EGL

NAL

AAS

NLY

STH

RAS

PAS

PCY

SSE

RGL

YSE

RAS

PLE

ULE

UPR

OAL

AME

TGL

YAS

NHI

SCY

SSE

RHI

SVA

LGL

YGL

YPR

OGL

NAS

PLE

UGL

ULY

STH

R


PRO

ARG

GLY

ARG

GLY

SER

PRO

LEU

PRO

PRO

PRO

ARG

GLU

ALA

SER

L397

�A3

98�

V399

R400

�

Q404

�

R416

�

Y461

�S4

62�

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

Chain F:

NAG1

NAG2

BMA3

�


Chain H:

NAG1

NAG2

BMA3

�


Chain J:

NAG1

NAG2

BMA3

�


Chain L:

NAG1

NAG2

BMA3

�


Chain N:

NAG1

NAG2

BMA3

�

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


Chain G:NA

G1NA

G2


Chain I:

NAG1

NAG2


Chain K:

NAG1

NAG2


Chain M:

NAG1

NAG2

�


Chain O:

NAG1

NAG2


4 Experimental information i○

Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, Not provided DepositorNumber of particles used 46757 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

) 45 DepositorMinimum defocus (nm) Not provided DepositorMaximum defocus (nm) Not provided DepositorMagnification 130000 DepositorImage detector GATAN K2 SUMMIT (4k x 4k) DepositorMaximum map value 0.123 DepositorMinimum map value -0.058 DepositorAverage map value 0.000 DepositorMap value standard deviation 0.003 DepositorRecommended contour level 0.0201 DepositorMap size (Å) 319.2, 319.2, 319.2 DepositorMap dimensions 300, 300, 300 DepositorMap angles (◦) 90.0, 90.0, 90.0 DepositorPixel spacing (Å) 1.064, 1.064, 1.064 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, CWB, CL

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 0.43 0/3350 0.65 4/4577 (0.1%)1 B 0.43 0/3350 0.65 4/4577 (0.1%)1 C 0.43 0/3350 0.65 4/4577 (0.1%)1 D 0.43 0/3350 0.65 4/4577 (0.1%)1 E 0.43 0/3350 0.65 4/4577 (0.1%)All All 0.43 0/16750 0.65 20/22885 (0.1%)

There are no bond length outliers.

All (20) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 B 312 ASP CB-CG-OD1 8.80 126.22 118.301 E 312 ASP CB-CG-OD1 8.79 126.21 118.301 C 312 ASP CB-CG-OD1 8.79 126.21 118.301 A 312 ASP CB-CG-OD1 8.73 126.15 118.301 D 312 ASP CB-CG-OD1 8.72 126.15 118.301 B 79 ASP CB-CG-OD1 7.92 125.43 118.301 C 79 ASP CB-CG-OD1 7.90 125.41 118.301 E 79 ASP CB-CG-OD1 7.89 125.41 118.301 D 79 ASP CB-CG-OD1 7.89 125.40 118.301 A 79 ASP CB-CG-OD1 7.88 125.39 118.301 C 19 LEU CA-CB-CG 5.59 128.17 115.301 B 19 LEU CA-CB-CG 5.59 128.16 115.301 A 19 LEU CA-CB-CG 5.58 128.14 115.301 D 19 LEU CA-CB-CG 5.58 128.14 115.301 E 19 LEU CA-CB-CG 5.57 128.12 115.301 E 298 LEU CA-CB-CG 5.15 127.15 115.301 A 298 LEU CA-CB-CG 5.15 127.14 115.301 C 298 LEU CA-CB-CG 5.14 127.12 115.301 B 298 LEU CA-CB-CG 5.14 127.11 115.30


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 Atoms Z Observed(o) Ideal(o)1 D 298 LEU CA-CB-CG 5.12 127.08 115.30

There are no chirality outliers.

There are no planarity outliers.

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 3260 0 3288 30 01 B 3260 0 3288 29 01 C 3260 0 3288 26 01 D 3260 0 3288 26 01 E 3260 0 3288 26 02 F 39 0 33 1 02 H 39 0 33 1 02 J 39 0 33 1 02 L 39 0 33 1 02 N 39 0 33 1 03 G 28 0 24 1 03 I 28 0 24 1 03 K 28 0 24 1 03 M 28 0 24 1 03 O 28 0 24 1 04 A 28 0 25 0 04 B 28 0 25 0 04 C 28 0 25 0 04 D 28 0 25 0 04 E 28 0 25 0 05 A 23 0 24 0 05 B 23 0 24 0 05 C 23 0 24 0 05 D 46 0 48 0 06 A 1 0 0 0 0All All 16891 0 16970 122 0

The all-atom clashscore is defined as the number of clashes found per 1000 atoms (including

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


hydrogen atoms). The all-atom clashscore for this structure is 4.

All (122) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:A:91:ASP:N 1:A:91:ASP:OD1 2.27 0.681:B:91:ASP:OD1 1:B:91:ASP:N 2.27 0.681:C:91:ASP:OD1 1:C:91:ASP:N 2.27 0.671:D:91:ASP:N 1:D:91:ASP:OD1 2.27 0.67

1:D:222:PHE:HE1 1:E:277:ALA:H 1.44 0.661:E:91:ASP:N 1:E:91:ASP:OD1 2.27 0.66

1:D:135:CYS:SG 1:D:136:SER:N 2.76 0.591:B:135:CYS:SG 1:B:136:SER:N 2.76 0.591:E:135:CYS:SG 1:E:136:SER:N 2.76 0.591:C:135:CYS:SG 1:C:136:SER:N 2.76 0.581:A:135:CYS:SG 1:A:136:SER:N 2.76 0.58

1:B:244:LEU:HD11 1:C:252:VAL:HG11 1.86 0.581:A:13:LEU:HB2 1:B:27:VAL:HG11 1.87 0.571:A:215:ILE:HG12 3:G:1:NAG:H82 1.88 0.561:B:215:ILE:HG12 3:I:1:NAG:H82 1.88 0.561:C:215:ILE:HG12 3:K:1:NAG:H82 1.88 0.561:D:164:ASN:ND2 2:L:1:NAG:O7 2.39 0.561:E:164:ASN:ND2 2:N:1:NAG:O7 2.39 0.561:E:215:ILE:HG12 3:O:1:NAG:H82 1.88 0.561:D:215:ILE:HG12 3:M:1:NAG:H82 1.88 0.551:B:164:ASN:ND2 2:H:1:NAG:O7 2.39 0.551:A:164:ASN:ND2 2:F:1:NAG:O7 2.39 0.551:C:164:ASN:ND2 2:J:1:NAG:O7 2.39 0.551:A:222:PHE:HE1 1:B:277:ALA:H 1.54 0.541:A:420:ARG:NH2 1:B:416:ARG:HD2 2.23 0.531:B:23:TYR:HE2 1:B:93:ILE:HA 1.77 0.491:A:23:TYR:HE2 1:A:93:ILE:HA 1.77 0.491:C:81:ASP:O 1:D:33:TRP:NE1 2.46 0.49

1:C:23:TYR:HE2 1:C:93:ILE:HA 1.77 0.481:D:227:LEU:HD21 1:D:273:LEU:HD21 1.95 0.481:D:23:TYR:HE2 1:D:93:ILE:HA 1.77 0.481:A:28:ARG:NE 1:A:162:ASP:OD1 2.47 0.48

1:A:227:LEU:HD21 1:A:273:LEU:HD21 1.95 0.481:D:53:GLU:OE2 1:D:218:ARG:NH2 2.47 0.481:E:53:GLU:OE2 1:E:218:ARG:NH2 2.47 0.481:B:53:GLU:OE2 1:B:218:ARG:NH2 2.47 0.471:A:424:ARG:HE 1:B:312:ASP:HB2 1.78 0.471:E:23:TYR:HE2 1:E:93:ILE:HA 1.77 0.47



Continued from previous page...


Clashoverlap (Å)

1:E:28:ARG:NE 1:E:162:ASP:OD1 2.47 0.471:D:160:ILE:HG13 1:D:208:ALA:HB2 1.97 0.471:D:28:ARG:NE 1:D:162:ASP:OD1 2.47 0.47

1:A:160:ILE:HG13 1:A:208:ALA:HB2 1.97 0.471:B:28:ARG:NE 1:B:162:ASP:OD1 2.47 0.471:C:28:ARG:NE 1:C:162:ASP:OD1 2.47 0.47

1:C:227:LEU:HD21 1:C:273:LEU:HD21 1.95 0.471:E:160:ILE:HG13 1:E:208:ALA:HB2 1.97 0.471:A:53:GLU:OE2 1:A:218:ARG:NH2 2.47 0.471:B:160:ILE:HG13 1:B:208:ALA:HB2 1.96 0.471:C:53:GLU:OE2 1:C:218:ARG:NH2 2.47 0.471:E:227:LEU:HD21 1:E:273:LEU:HD21 1.95 0.471:B:227:LEU:HD21 1:B:273:LEU:HD21 1.95 0.471:C:160:ILE:HG13 1:C:208:ALA:HB2 1.97 0.471:C:12:LEU:HD13 1:C:12:LEU:HA 1.77 0.471:C:13:LEU:HB2 1:D:27:VAL:HG11 1.96 0.461:D:424:ARG:HE 1:E:312:ASP:HB2 1.81 0.461:A:27:VAL:HG11 1:E:13:LEU:HB2 1.97 0.461:A:108:LYS:HB2 1:B:105:ASP:OD1 2.16 0.461:B:431:TYR:HE2 1:C:311:GLN:HB2 1.82 0.451:D:234:LEU:HD22 1:D:258:LEU:HD11 1.99 0.451:A:234:LEU:HD22 1:A:258:LEU:HD11 1.99 0.451:B:234:LEU:HD22 1:B:258:LEU:HD11 1.99 0.451:C:234:LEU:HD22 1:C:258:LEU:HD11 1.99 0.451:E:170:SER:OG 1:E:172:GLU:OE1 2.35 0.451:D:170:SER:OG 1:D:172:GLU:OE1 2.35 0.451:E:234:LEU:HD22 1:E:258:LEU:HD11 1.99 0.451:A:277:ALA:H 1:E:222:PHE:HE1 1.65 0.441:C:170:SER:OG 1:C:172:GLU:OE1 2.35 0.441:A:170:SER:OG 1:A:172:GLU:OE1 2.35 0.441:B:234:LEU:HD12 1:B:262:TYR:HD1 1.83 0.441:C:234:LEU:HD12 1:C:262:TYR:HD1 1.83 0.441:D:12:LEU:HD13 1:D:12:LEU:HA 1.77 0.441:B:170:SER:OG 1:B:172:GLU:OE1 2.35 0.431:C:141:ASN:OD1 1:C:141:ASN:N 2.52 0.431:A:234:LEU:HD12 1:A:262:TYR:HD1 1.83 0.431:A:12:LEU:HD13 1:A:12:LEU:HA 1.77 0.431:E:158:HIS:HB3 1:E:162:ASP:HB3 2.01 0.431:E:234:LEU:HD12 1:E:262:TYR:HD1 1.83 0.431:D:234:LEU:HD12 1:D:262:TYR:HD1 1.83 0.421:B:158:HIS:HB3 1:B:162:ASP:HB3 2.01 0.42





Clashoverlap (Å)

1:C:158:HIS:HB3 1:C:162:ASP:HB3 2.01 0.421:A:320:TRP:HA 1:A:323:HIS:HB3 2.01 0.421:D:158:HIS:HB3 1:D:162:ASP:HB3 2.01 0.421:D:141:ASN:N 1:D:141:ASN:OD1 2.52 0.421:A:116:TYR:HA 1:A:116:TYR:HD1 1.78 0.421:A:158:HIS:HB3 1:A:162:ASP:HB3 2.01 0.421:A:141:ASN:N 1:A:141:ASN:OD1 2.52 0.42

1:C:39:VAL:HG12 1:C:68:TRP:HB3 2.02 0.421:E:116:TYR:HD1 1:E:116:TYR:HA 1.78 0.421:B:141:ASN:OD1 1:B:141:ASN:N 2.52 0.421:B:12:LEU:HA 1:B:12:LEU:HD13 1.77 0.411:E:12:LEU:HA 1:E:12:LEU:HD13 1.77 0.411:C:320:TRP:HA 1:C:323:HIS:HB3 2.01 0.411:D:320:TRP:HA 1:D:323:HIS:HB3 2.01 0.411:A:192:VAL:HG22 1:A:214:VAL:HG12 2.02 0.411:E:192:VAL:HG22 1:E:214:VAL:HG12 2.02 0.411:C:192:VAL:HG22 1:C:214:VAL:HG12 2.02 0.411:C:41:ILE:HD13 1:C:153:PHE:HD2 1.86 0.411:E:141:ASN:N 1:E:141:ASN:OD1 2.52 0.411:A:41:ILE:HD13 1:A:153:PHE:HD2 1.86 0.411:D:128:PRO:HD3 1:E:156:TRP:CE2 2.55 0.411:D:41:ILE:HD13 1:D:153:PHE:HD2 1.86 0.411:A:105:ASP:HB3 1:A:132:VAL:HG21 2.03 0.401:A:39:VAL:HG12 1:A:68:TRP:HB3 2.02 0.401:D:105:ASP:HB3 1:D:132:VAL:HG21 2.03 0.401:D:192:VAL:HG22 1:D:214:VAL:HG12 2.02 0.401:E:105:ASP:HB3 1:E:132:VAL:HG21 2.03 0.401:B:320:TRP:HA 1:B:323:HIS:HB3 2.02 0.401:B:41:ILE:HD13 1:B:153:PHE:HD2 1.86 0.401:B:39:VAL:HG12 1:B:68:TRP:HB3 2.02 0.401:E:39:VAL:HG12 1:E:68:TRP:HB3 2.02 0.401:B:105:ASP:HB3 1:B:132:VAL:HG21 2.03 0.401:C:105:ASP:HB3 1:C:132:VAL:HG21 2.03 0.401:C:116:TYR:HA 1:C:116:TYR:HD1 1.78 0.401:E:320:TRP:HA 1:E:323:HIS:HB3 2.02 0.401:A:145:ASP:OD1 1:A:145:ASP:N 2.55 0.401:C:145:ASP:N 1:C:145:ASP:OD1 2.55 0.40

1:D:145:ASP:OD1 1:D:145:ASP:N 2.54 0.401:E:41:ILE:HD13 1:E:153:PHE:HD2 1.86 0.401:B:116:TYR:HA 1:B:116:TYR:HD1 1.78 0.401:B:145:ASP:OD1 1:B:145:ASP:N 2.55 0.40





Clashoverlap (Å)

1:A:128:PRO:HD3 1:B:156:TRP:CE2 2.56 0.401:D:39:VAL:HG12 1:D:68:TRP:HB3 2.02 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 391/489 (80%) 371 (95%) 20 (5%) 0 100 100

1 B 391/489 (80%) 371 (95%) 20 (5%) 0 100 100

1 C 391/489 (80%) 371 (95%) 20 (5%) 0 100 100

1 D 391/489 (80%) 371 (95%) 20 (5%) 0 100 100

1 E 391/489 (80%) 370 (95%) 21 (5%) 0 100 100

All All 1955/2445 (80%) 1854 (95%) 101 (5%) 0 100 100

There are no Ramachandran outliers to report.

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 365/445 (82%) 363 (100%) 2 (0%) 88 96

1 B 365/445 (82%) 363 (100%) 2 (0%) 88 96Continued on next page...

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

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

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


Continued from previous page...Mol Chain Analysed Rotameric Outliers Percentiles

1 C 365/445 (82%) 363 (100%) 2 (0%) 88 96

1 D 365/445 (82%) 363 (100%) 2 (0%) 88 96

1 E 365/445 (82%) 363 (100%) 2 (0%) 88 96

All All 1825/2225 (82%) 1815 (100%) 10 (0%) 89 96

All (10) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 A 91 ASP1 A 315 ARG1 B 91 ASP1 B 315 ARG1 C 91 ASP1 C 315 ARG1 D 91 ASP1 D 315 ARG1 E 91 ASP1 E 315 ARG

Some sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (8) suchsidechains are listed below:

Mol Chain Res Type1 A 82 ASN1 B 82 ASN1 B 309 HIS1 C 82 ASN1 C 101 ASN1 D 82 ASN1 D 101 ASN1 E 82 ASN

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.

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

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


5.5 Carbohydrates i○

25 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 F 1 2 14,14,15 0.70 1 (7%) 17,19,21 2.73 2 (11%)2 NAG F 2 2 14,14,15 0.18 0 17,19,21 0.74 1 (5%)2 BMA F 3 2 11,11,12 0.61 0 15,15,17 0.93 1 (6%)3 NAG G 1 1,3 14,14,15 0.62 1 (7%) 17,19,21 2.46 3 (17%)3 NAG G 2 3 14,14,15 0.29 0 17,19,21 0.44 02 NAG H 1 2 14,14,15 0.68 1 (7%) 17,19,21 2.72 2 (11%)2 NAG H 2 2 14,14,15 0.19 0 17,19,21 0.74 1 (5%)2 BMA H 3 2 11,11,12 0.61 0 15,15,17 0.93 1 (6%)3 NAG I 1 1,3 14,14,15 0.62 1 (7%) 17,19,21 2.46 3 (17%)3 NAG I 2 3 14,14,15 0.28 0 17,19,21 0.43 02 NAG J 1 2 14,14,15 0.69 1 (7%) 17,19,21 2.72 2 (11%)2 NAG J 2 2 14,14,15 0.20 0 17,19,21 0.74 1 (5%)2 BMA J 3 2 11,11,12 0.61 0 15,15,17 0.93 1 (6%)3 NAG K 1 1,3 14,14,15 0.63 1 (7%) 17,19,21 2.46 3 (17%)3 NAG K 2 3 14,14,15 0.28 0 17,19,21 0.44 02 NAG L 1 2 14,14,15 0.70 1 (7%) 17,19,21 2.72 2 (11%)2 NAG L 2 2 14,14,15 0.18 0 17,19,21 0.74 1 (5%)2 BMA L 3 2 11,11,12 0.60 0 15,15,17 0.94 1 (6%)3 NAG M 1 1,3 14,14,15 0.63 1 (7%) 17,19,21 2.46 3 (17%)3 NAG M 2 3 14,14,15 0.29 0 17,19,21 0.43 02 NAG N 1 2 14,14,15 0.69 1 (7%) 17,19,21 2.73 2 (11%)2 NAG N 2 2 14,14,15 0.19 0 17,19,21 0.74 1 (5%)2 BMA N 3 2 11,11,12 0.61 0 15,15,17 0.94 1 (6%)3 NAG O 1 1,3 14,14,15 0.62 1 (7%) 17,19,21 2.46 3 (17%)3 NAG O 2 3 14,14,15 0.27 0 17,19,21 0.44 0

In the following table, the Chirals column lists the number of chiral outliers, the number of chiral



centers 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 F 1 2 - 1/6/23/26 0/1/1/12 NAG F 2 2 - 2/6/23/26 0/1/1/12 BMA F 3 2 - 0/2/19/22 0/1/1/13 NAG G 1 1,3 - 2/6/23/26 0/1/1/13 NAG G 2 3 - 0/6/23/26 0/1/1/12 NAG H 1 2 - 1/6/23/26 0/1/1/12 NAG H 2 2 - 2/6/23/26 0/1/1/12 BMA H 3 2 - 0/2/19/22 0/1/1/13 NAG I 1 1,3 - 2/6/23/26 0/1/1/13 NAG I 2 3 - 0/6/23/26 0/1/1/12 NAG J 1 2 - 1/6/23/26 0/1/1/12 NAG J 2 2 - 2/6/23/26 0/1/1/12 BMA J 3 2 - 0/2/19/22 0/1/1/13 NAG K 1 1,3 - 2/6/23/26 0/1/1/13 NAG K 2 3 - 0/6/23/26 0/1/1/12 NAG L 1 2 - 1/6/23/26 0/1/1/12 NAG L 2 2 - 2/6/23/26 0/1/1/12 BMA L 3 2 - 0/2/19/22 0/1/1/13 NAG M 1 1,3 - 2/6/23/26 0/1/1/13 NAG M 2 3 - 0/6/23/26 0/1/1/12 NAG N 1 2 - 1/6/23/26 0/1/1/12 NAG N 2 2 - 2/6/23/26 0/1/1/12 BMA N 3 2 - 0/2/19/22 0/1/1/13 NAG O 1 1,3 - 2/6/23/26 0/1/1/13 NAG O 2 3 - 0/6/23/26 0/1/1/1

All (10) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)3 M 1 NAG O4-C4 -2.27 1.37 1.433 K 1 NAG O4-C4 -2.26 1.37 1.433 O 1 NAG O4-C4 -2.25 1.37 1.433 G 1 NAG O4-C4 -2.24 1.37 1.432 L 1 NAG O4-C4 -2.24 1.37 1.433 I 1 NAG O4-C4 -2.24 1.37 1.432 F 1 NAG O4-C4 -2.23 1.37 1.432 N 1 NAG O4-C4 -2.23 1.37 1.43



Continued from previous page...Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)2 J 1 NAG O4-C4 -2.23 1.37 1.432 H 1 NAG O4-C4 -2.18 1.37 1.43


Mol Chain Res Type Atoms Z Observed(o) Ideal(o)2 F 1 NAG O4-C4-C3 10.39 134.36 110.352 N 1 NAG O4-C4-C3 10.38 134.34 110.352 J 1 NAG O4-C4-C3 10.36 134.29 110.352 L 1 NAG O4-C4-C3 10.35 134.29 110.352 H 1 NAG O4-C4-C3 10.34 134.26 110.353 K 1 NAG O4-C4-C3 8.86 130.84 110.353 G 1 NAG O4-C4-C3 8.86 130.83 110.353 M 1 NAG O4-C4-C3 8.85 130.82 110.353 I 1 NAG O4-C4-C3 8.85 130.80 110.353 O 1 NAG O4-C4-C3 8.84 130.79 110.352 F 1 NAG O4-C4-C5 -3.89 99.63 109.302 H 1 NAG O4-C4-C5 -3.87 99.68 109.302 N 1 NAG O4-C4-C5 -3.87 99.68 109.302 L 1 NAG O4-C4-C5 -3.87 99.69 109.302 J 1 NAG O4-C4-C5 -3.86 99.71 109.303 K 1 NAG O4-C4-C5 -3.38 100.91 109.303 M 1 NAG O4-C4-C5 -3.37 100.92 109.303 I 1 NAG O4-C4-C5 -3.37 100.94 109.303 O 1 NAG O4-C4-C5 -3.36 100.96 109.303 G 1 NAG O4-C4-C5 -3.36 100.96 109.303 G 1 NAG C1-O5-C5 3.18 116.51 112.193 K 1 NAG C1-O5-C5 3.16 116.47 112.193 I 1 NAG C1-O5-C5 3.15 116.46 112.193 O 1 NAG C1-O5-C5 3.14 116.44 112.193 M 1 NAG C1-O5-C5 3.13 116.44 112.192 F 2 NAG C1-O5-C5 2.29 115.30 112.192 H 2 NAG C1-O5-C5 2.29 115.29 112.192 J 2 NAG C1-O5-C5 2.27 115.27 112.192 L 2 NAG C1-O5-C5 2.27 115.26 112.192 N 2 NAG C1-O5-C5 2.26 115.26 112.192 F 3 BMA C1-O5-C5 2.16 115.11 112.192 N 3 BMA C1-O5-C5 2.14 115.09 112.192 L 3 BMA C1-O5-C5 2.14 115.09 112.192 H 3 BMA C1-O5-C5 2.13 115.08 112.192 J 3 BMA C1-O5-C5 2.13 115.07 112.19



All (25) torsion outliers are listed below:

Mol Chain Res Type Atoms3 K 1 NAG O5-C5-C6-O63 M 1 NAG O5-C5-C6-O63 I 1 NAG O5-C5-C6-O63 O 1 NAG O5-C5-C6-O63 G 1 NAG O5-C5-C6-O63 K 1 NAG C4-C5-C6-O63 M 1 NAG C4-C5-C6-O63 I 1 NAG C4-C5-C6-O63 O 1 NAG C4-C5-C6-O63 G 1 NAG C4-C5-C6-O62 J 2 NAG O5-C5-C6-O62 F 2 NAG O5-C5-C6-O62 N 2 NAG O5-C5-C6-O62 L 2 NAG O5-C5-C6-O62 H 2 NAG O5-C5-C6-O62 J 2 NAG C4-C5-C6-O62 N 2 NAG C4-C5-C6-O62 L 2 NAG C4-C5-C6-O62 F 2 NAG C4-C5-C6-O62 H 2 NAG C4-C5-C6-O62 J 1 NAG O5-C5-C6-O62 N 1 NAG O5-C5-C6-O62 F 1 NAG O5-C5-C6-O62 H 1 NAG O5-C5-C6-O62 L 1 NAG O5-C5-C6-O6

There are no ring outliers.

10 monomers are involved in 10 short contacts:

Mol Chain Res Type Clashes Symm-Clashes3 K 1 NAG 1 03 M 1 NAG 1 02 N 1 NAG 1 02 F 1 NAG 1 02 H 1 NAG 1 02 J 1 NAG 1 03 I 1 NAG 1 03 O 1 NAG 1 02 L 1 NAG 1 03 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 F

Bond lengths Bond angles

Torsions Rings

Oligosaccharide Chain H


Torsions Rings


Oligosaccharide Chain J


Torsions Rings

Oligosaccharide Chain L


Torsions Rings


Oligosaccharide Chain N


Torsions Rings


Oligosaccharide Chain G


Torsions Rings


Oligosaccharide Chain I


Torsions Rings


Oligosaccharide Chain K


Torsions Rings


Oligosaccharide Chain M


Torsions Rings


Oligosaccharide Chain O


Torsions Rings

5.6 Ligand geometry i○

Of 16 ligands modelled in this entry, 1 is monoatomic - leaving 15 for Mogul analysis.

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).


4 NAG B 502 - 15,15,15 0.15 0 21,21,21 0.22 04 NAG D 502 - 15,15,15 0.15 0 21,21,21 0.22 05 CWB C 508 - 22,26,26 4.84 11 (50%) 27,38,38 2.19 9 (33%)




5 CWB A 508 - 22,26,26 4.82 12 (54%) 27,38,38 2.16 9 (33%)5 CWB D 508 - 22,26,26 4.83 10 (45%) 27,38,38 2.16 9 (33%)4 NAG A 502 - 15,15,15 0.15 0 21,21,21 0.22 05 CWB B 508 - 22,26,26 4.85 11 (50%) 27,38,38 2.17 9 (33%)4 NAG E 502 - 15,15,15 0.15 0 21,21,21 0.22 04 NAG C 501 - 13,13,15 0.34 0 14,17,21 1.07 1 (7%)4 NAG D 501 - 13,13,15 0.33 0 14,17,21 1.06 1 (7%)4 NAG A 501 - 13,13,15 0.33 0 14,17,21 1.07 1 (7%)4 NAG B 501 - 13,13,15 0.33 0 14,17,21 1.07 1 (7%)4 NAG C 502 - 15,15,15 0.16 0 21,21,21 0.22 04 NAG E 501 - 13,13,15 0.33 0 14,17,21 1.07 1 (7%)5 CWB D 509 - 22,26,26 4.87 12 (54%) 27,38,38 2.15 10 (37%)

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 Rings4 NAG B 502 - - 2/6/26/26 0/1/1/14 NAG D 502 - - 2/6/26/26 0/1/1/15 CWB C 508 - - 0/4/30/30 0/5/4/45 CWB A 508 - - 0/4/30/30 0/5/4/45 CWB D 508 - - 0/4/30/30 0/5/4/44 NAG A 502 - - 2/6/26/26 0/1/1/15 CWB B 508 - - 0/4/30/30 0/5/4/44 NAG E 502 - - 2/6/26/26 0/1/1/14 NAG C 501 - - 3/6/19/26 0/1/1/14 NAG D 501 - - 3/6/19/26 0/1/1/14 NAG A 501 - - 3/6/19/26 0/1/1/14 NAG B 501 - - 3/6/19/26 0/1/1/14 NAG C 502 - - 2/6/26/26 0/1/1/14 NAG E 501 - - 3/6/19/26 0/1/1/15 CWB D 509 - - 0/4/30/30 0/5/4/4

All (56) bond length outliers are listed below:


Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)5 D 509 CWB C01-N02 -18.10 1.18 1.475 B 508 CWB C01-N02 -18.01 1.19 1.475 D 508 CWB C01-N02 -17.97 1.19 1.475 A 508 CWB C01-N02 -17.91 1.19 1.475 C 508 CWB C01-N02 -17.89 1.19 1.475 C 508 CWB C08-C09 -6.36 1.42 1.525 D 508 CWB C08-C09 -6.28 1.43 1.525 B 508 CWB C08-C09 -6.27 1.43 1.525 D 509 CWB C08-C09 -6.10 1.43 1.525 A 508 CWB C08-C09 -5.95 1.43 1.525 A 508 CWB C09-N11 5.86 1.58 1.465 D 509 CWB C09-N11 5.84 1.58 1.465 B 508 CWB C09-N11 5.74 1.58 1.465 D 508 CWB C09-N11 5.70 1.58 1.465 C 508 CWB C09-N11 5.66 1.58 1.465 A 508 CWB C12-N11 5.11 1.45 1.345 D 509 CWB C12-N11 5.07 1.45 1.345 B 508 CWB C12-N11 4.89 1.44 1.345 C 508 CWB C10-C09 -4.88 1.45 1.525 C 508 CWB C12-N11 4.85 1.44 1.345 D 508 CWB C12-N11 4.83 1.44 1.345 D 508 CWB C10-C09 -4.80 1.45 1.525 B 508 CWB C10-C09 -4.76 1.45 1.525 D 509 CWB C10-C09 -4.70 1.45 1.525 A 508 CWB C10-C09 -4.67 1.45 1.525 D 509 CWB C14-C12 4.04 1.56 1.505 C 508 CWB C07-N02 -4.02 1.43 1.475 B 508 CWB C14-C12 4.01 1.56 1.505 A 508 CWB C14-C12 3.99 1.56 1.505 D 509 CWB C07-N02 -3.99 1.43 1.475 D 508 CWB C07-N02 -3.96 1.43 1.475 C 508 CWB C14-C12 3.91 1.56 1.505 B 508 CWB C07-N02 -3.88 1.43 1.475 D 508 CWB C14-C12 3.87 1.56 1.505 A 508 CWB C07-N02 -3.68 1.43 1.475 C 508 CWB C05-C04 3.64 1.62 1.535 B 508 CWB C05-C04 3.62 1.62 1.535 D 508 CWB C05-C04 3.60 1.62 1.535 D 509 CWB C05-C04 3.57 1.62 1.535 A 508 CWB C05-C04 3.54 1.62 1.535 C 508 CWB C10-C03 2.77 1.58 1.535 D 508 CWB C10-C03 2.68 1.58 1.535 B 508 CWB C10-C03 2.64 1.58 1.53



Continued from previous page...Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)5 D 509 CWB C10-C03 2.61 1.58 1.535 A 508 CWB C10-C03 2.58 1.58 1.535 A 508 CWB C14-N15 -2.17 1.33 1.355 C 508 CWB C05-C06 2.13 1.58 1.535 D 509 CWB C05-C06 2.11 1.58 1.535 B 508 CWB C05-C06 2.09 1.58 1.535 A 508 CWB C05-C06 2.08 1.58 1.535 D 509 CWB C14-N15 -2.07 1.33 1.355 D 508 CWB C05-C06 2.07 1.58 1.535 A 508 CWB C21-C22 2.03 1.41 1.365 B 508 CWB C21-C22 2.03 1.41 1.365 C 508 CWB C21-C22 2.03 1.41 1.365 D 509 CWB C21-C22 2.03 1.41 1.36


Mol Chain Res Type Atoms Z Observed(o) Ideal(o)5 A 508 CWB C08-C09-C10 5.58 116.05 111.135 D 509 CWB C08-C09-C10 5.41 115.90 111.135 B 508 CWB C08-C09-C10 5.31 115.80 111.135 C 508 CWB C01-N02-C03 5.20 117.36 113.165 D 508 CWB C08-C09-C10 5.16 115.68 111.135 C 508 CWB C08-C09-C10 4.85 115.40 111.135 D 508 CWB C01-N02-C03 4.81 117.05 113.165 C 508 CWB C09-C08-C07 4.79 119.09 112.165 B 508 CWB C01-N02-C03 4.59 116.86 113.165 A 508 CWB C01-N02-C03 4.36 116.68 113.165 D 508 CWB C09-C08-C07 4.27 118.33 112.165 B 508 CWB C09-C08-C07 4.21 118.24 112.165 D 509 CWB C01-N02-C03 4.19 116.54 113.165 D 509 CWB C09-C08-C07 3.87 117.75 112.165 A 508 CWB C09-C08-C07 3.77 117.62 112.165 C 508 CWB C09-C10-C03 3.30 116.93 112.165 A 508 CWB C01-N02-C07 3.21 115.75 113.165 B 508 CWB C09-C10-C03 3.19 116.77 112.165 D 509 CWB C09-C10-C03 3.18 116.76 112.165 D 508 CWB C09-C10-C03 3.16 116.73 112.165 A 508 CWB C09-C10-C03 3.12 116.67 112.164 B 501 NAG C2-N2-C7 3.10 127.32 122.904 A 501 NAG C2-N2-C7 3.10 127.31 122.904 E 501 NAG C2-N2-C7 3.09 127.31 122.904 D 501 NAG C2-N2-C7 3.09 127.30 122.90



Continued from previous page...Mol Chain Res Type Atoms Z Observed(o) Ideal(o)4 C 501 NAG C2-N2-C7 3.08 127.29 122.905 D 509 CWB C01-N02-C07 3.02 115.59 113.165 D 509 CWB C08-C07-N02 2.75 114.96 109.485 D 508 CWB C01-N02-C07 2.70 115.34 113.165 D 509 CWB C07-N02-C03 2.67 114.61 109.945 A 508 CWB C08-C07-N02 2.65 114.75 109.485 B 508 CWB C08-C07-N02 2.59 114.63 109.485 B 508 CWB C01-N02-C07 2.55 115.22 113.165 D 508 CWB C07-N02-C03 2.55 114.41 109.945 B 508 CWB C07-N02-C03 2.55 114.40 109.945 C 508 CWB C07-N02-C03 2.51 114.34 109.945 A 508 CWB C07-N02-C03 2.47 114.27 109.945 D 508 CWB C08-C07-N02 2.46 114.37 109.485 C 508 CWB C01-N02-C07 2.40 115.10 113.165 A 508 CWB C08-C07-C06 -2.31 109.11 113.075 B 508 CWB C08-C07-C06 -2.31 109.11 113.075 C 508 CWB C08-C07-C06 -2.30 109.14 113.075 D 508 CWB C12-C14-N15 2.28 126.28 120.575 C 508 CWB C08-C07-N02 2.27 113.99 109.485 B 508 CWB C12-C14-N15 2.25 126.22 120.575 D 509 CWB C08-C07-C06 -2.24 109.23 113.075 C 508 CWB C12-C14-N15 2.23 126.16 120.575 D 508 CWB C08-C07-C06 -2.22 109.27 113.075 D 509 CWB C12-C14-N15 2.11 125.86 120.575 A 508 CWB C12-C14-N15 2.07 125.75 120.575 D 509 CWB C06-C07-N02 -2.01 107.00 111.10


All (25) torsion outliers are listed below:

Mol Chain Res Type Atoms4 C 501 NAG C4-C5-C6-O64 C 501 NAG O5-C5-C6-O64 D 501 NAG C4-C5-C6-O64 D 501 NAG O5-C5-C6-O64 A 501 NAG C4-C5-C6-O64 A 501 NAG O5-C5-C6-O64 B 501 NAG C4-C5-C6-O64 B 501 NAG O5-C5-C6-O64 E 501 NAG C4-C5-C6-O64 E 501 NAG O5-C5-C6-O64 B 502 NAG O5-C5-C6-O6



Continued from previous page...Mol Chain Res Type Atoms4 D 502 NAG O5-C5-C6-O64 A 502 NAG O5-C5-C6-O64 E 502 NAG O5-C5-C6-O64 C 502 NAG O5-C5-C6-O64 B 502 NAG C4-C5-C6-O64 D 502 NAG C4-C5-C6-O64 A 502 NAG C4-C5-C6-O64 E 502 NAG C4-C5-C6-O64 C 502 NAG C4-C5-C6-O64 C 501 NAG C3-C2-N2-C74 D 501 NAG C3-C2-N2-C74 A 501 NAG C3-C2-N2-C74 B 501 NAG C3-C2-N2-C74 E 501 NAG C3-C2-N2-C7

There are no ring outliers.

No monomer is involved in short contacts.

The following is a two-dimensional graphical depiction of Mogul quality analysis of bond lengths,bond angles, torsion angles, and ring geometry for all instances of the Ligand of Interest. Inaddition, ligands with molecular weight > 250 and outliers as shown on the validation Tables willalso be included. For torsion angles, if less then 5% of the Mogul distribution of torsion angles iswithin 10 degrees of the torsion angle in question, then that torsion angle is considered an outlier.Any bond that is central to one or more torsion angles identified as an outlier by Mogul will behighlighted in the graph. For rings, the root-mean-square deviation (RMSD) between the ringin question and similar rings identified by Mogul is calculated over all ring torsion angles. If theaverage RMSD is greater than 60 degrees and the minimal RMSD between the ring in question andany Mogul-identified rings is also greater than 60 degrees, then that ring is considered an outlier.The outliers are highlighted in purple. The color gray indicates Mogul did not find sufficientequivalents in the CSD to analyse the geometry.


Ligand CWB C 508


Torsions Rings

Ligand CWB A 508


Torsions Rings


Ligand CWB D 508


Torsions Rings

Ligand CWB B 508


Torsions Rings


Ligand CWB D 509


Torsions Rings

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-0469. These are intended to permitvisual inspection of the internal detail of the map and identification of artifacts.

6.1 Orthogonal projections i○

X Y Z

The images above show the map projected in three orthogonal projections, in greyscale.

6.2 Central slices i○

X Y Z

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

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

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

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


6.3 Largest variance slices i○

X Index: 140 Y Index: 164 Z Index: 118

The images above show the highest variance slices of the map in three orthogonal directions, ingreyscale.

6.4 Orthogonal surface views i○

X Y Z

The images above show the 3D surface view of the map at the recommended contour level 0.0201.This in conjunction with the slice images can indicate whether an appropriate contour level hasbeen selected.

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

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_0469_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 97 nm3; this corresponds to an approximate massof 87 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○

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 resolutionfor single-particle and subtomogram-averaging methods. The shape of the curve depends on theimposed symmetry, mask and whether or not the two 3D reconstructions used were processed froma common reference. The reported resolution is shown as a black line. Curves are displayed for3σ, 1-bit and 1/2-bit in addition to lines showing the 0.143 gold standard cut-off, 0.333 cut-off andlegacy 0.5 cut-off.

8.1 Resolution estimates i○

These are global values for the map.

Source Criterion Resolution estimate (Å)Reported value FSC 0.143 CUT-OFF 2.92Calculated FSC FSC 0.5 CUT-OFF 4.08Calculated FSC FSC 1 BIT CUT-OFF 3.87Calculated FSC FSC 0.33 CUT-OFF 3.82Calculated FSC FSC 1/2 BIT CUT-OFF 3.66Calculated FSC FSC 0.143 CUT-OFF 3.53Calculated FSC FSC 3 SIGMA CUT-OFF 3.09

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

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


8.2 Calculated FSC i○

This FSC information has been calculated from the half-maps provided by the depositor. As werequest un-masked, un-processed half-maps the curve may be significantly different to the author-provided FSC.

8.3 Author-provided FSC i○

This section was not generated. The author did not provide an FSC file.

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

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


9 Map-model fit i○

This section contains information regarding the fit between EMDB map EMD-0469 and PDBmodel 6NP0. Per-residue inclusion information can be found in section 3 on page 8.

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 0.0201at 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, 85% of all backbone atoms, 76% of all non-hydrogen atoms,are inside the map.

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

Full wwPDB/EMDataBank EM Map/Model Validation Report · 2019. 7. 26. · Full wwPDB/EMDataBank EM...

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