Full wwPDB X-ray Structure Validation Report i○

Mar 9, 2018 – 06:19 am GMT

PDB ID : 4GBRTitle : N-Terminal T4 Lysozyme Fusion Facilitates Crystallization of a G Protein

Coupled ReceptorAuthors : Zou, Y.; Weis, W.I.; Kobilka, B.K.

Deposited on : 2012-07-27Resolution : 3.99 Å(reported)

This is a Full wwPDB X-ray Structure Validation Report for a publicly released PDB entry.

We welcome your comments at validation@mail.wwpdb.orgA user guide is available at

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

MolProbity : 4.02b-467Mogul : 1.7.3 (157068), CSD as539be (2018)

Xtriage (Phenix) : 1.13EDS : trunk30967

Percentile statistics : 20171227.v01 (using entries in the PDB archive December 27th 2017)Refmac : 5.8.0158CCP4 : 7.0 (Gargrove)

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

Validation Pipeline (wwPDB-VP) : trunk30967

Page 2 Full wwPDB X-ray Structure Validation Report 4GBR

1 Overall quality at a glance i○

The following experimental techniques were used to determine the structure:X-RAY DIFFRACTION

The reported resolution of this entry is 3.99 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)

Similar resolution(#Entries, resolution range(Å))

Rfree 111664 1008 (4.38-3.62)Clashscore 122126 1012 (4.34-3.66)

Ramachandran outliers 120053 1000 (4.36-3.64)Sidechain outliers 120020 1023 (4.38-3.62)RSRZ outliers 108989 1107 (4.40-3.60)

The table below summarises the geometric issues observed across the polymeric chains and their fitto the electron density. The red, orange, yellow and green segments on the lower bar indicate thefraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria. 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 theelectron density. The numeric value is given above the bar.

Mol Chain Length Quality of chain

1 A 309

2 B 163

Page 3 Full wwPDB X-ray Structure Validation Report 4GBR

2 Entry composition i○

There are 3 unique types of molecules in this entry. The entry contains 3610 atoms, of which 0are hydrogens and 0 are deuteriums.

In the tables below, the ZeroOcc column contains the number of atoms modelled with zero occu-pancy, the AltConf column contains the number of residues with at least one atom in alternateconformation and the Trace column contains the number of residues modelled with at most 2atoms.

• Molecule 1 is a protein called Beta-2 adrenergic receptor.

Mol Chain Residues Atoms ZeroOcc AltConf Trace

1 A 286 Total C N O S2303 1532 364 389 18 0 0 0

There are 31 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceA 96 THR MET ENGINEERED MUTATION UNP P07550A 98 THR MET ENGINEERED MUTATION UNP P07550A 187 GLU ASN ENGINEERED MUTATION UNP P07550A ? - LYS DELETION UNP P07550A ? - SER DELETION UNP P07550A ? - GLU DELETION UNP P07550A ? - GLY DELETION UNP P07550A ? - ARG DELETION UNP P07550A ? - PHE DELETION UNP P07550A ? - HIS DELETION UNP P07550A ? - VAL DELETION UNP P07550A ? - GLN DELETION UNP P07550A ? - ASN DELETION UNP P07550A ? - LEU DELETION UNP P07550A ? - SER DELETION UNP P07550A ? - GLN DELETION UNP P07550A ? - VAL DELETION UNP P07550A ? - GLU DELETION UNP P07550A ? - GLN DELETION UNP P07550A ? - ASP DELETION UNP P07550A ? - GLY DELETION UNP P07550A ? - ARG DELETION UNP P07550A ? - THR DELETION UNP P07550A ? - GLY DELETION UNP P07550A ? - HIS DELETION UNP P07550A ? - GLY DELETION UNP P07550A ? - LEU DELETION UNP P07550

Continued on next page...

Page 4 Full wwPDB X-ray Structure Validation Report 4GBR

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

A ? - ARG DELETION UNP P07550A ? - ARG DELETION UNP P07550A ? - SER DELETION UNP P07550A ? - SER DELETION UNP P07550

• Molecule 2 is a protein called Lysozyme.

Mol Chain Residues Atoms ZeroOcc AltConf Trace

2 B 162 Total C N O S1285 809 234 238 4 0 0 0

There are 5 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceB 1001 GLY - EXPRESSION TAG UNP P00720B 1054 THR CYS CONFLICT UNP P00720B 1097 ALA CYS CONFLICT UNP P00720B 1162 ALA - EXPRESSION TAG UNP P00720B 1163 ALA - EXPRESSION TAG UNP P00720

• Molecule 3 is (2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol (three-lettercode: CAU) (formula: C18H22N2O2).

Mol Chain Residues Atoms ZeroOcc AltConf

3 A 1 Total C N O22 18 2 2 0 0

Page 5 Full wwPDB X-ray Structure Validation Report 4GBR

3 Residue-property plots i○

These plots are drawn for all protein, RNA and DNA chains in the entry. The first graphic fora chain summarises the proportions of the various outlier classes displayed in the second graphic.The second graphic shows the sequence view annotated by issues in geometryand electron density.Residues are color-coded according to the number of geometric quality criteria for which theycontain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. A red dotabove a residue indicates a poor fit to the electron density (RSRZ > 2). Stretches of 2 or moreconsecutive residues without any outlier are shown as a green connector. Residues present in thesample, but not in the model, are shown in grey.

• Molecule 1: Beta-2 adrenergic receptor

Chain A:

D29

W32

V33

V34

G35

M36

G37

I38

V39

M40

S41

L42

I43

V44

L53

L64

Q65

T66

V67

T68

N69

Y70

F71

I72

C77

V81

V86

A91

L95

F108

W109

T110

S111

I112

E122

V126

R131

I135•

K140•

Y141•

Q142•

S143•

L144

L145•

T146•

K147

N148

K149

V152

I153

V157

L167

P168

I169

Q170

M171•

H172

W173

Y174

R175

C184

E188•

D192•

N196

S207

V210

P211

V218

Y219

S220

R221

V222

F223

Q224

E225

A226

K227

R228

Q229

L230

Q231

K232

I233

D234

K235

F236

C237

E240

H241

K245

I249

I250

M251

G252

T255

L256

C257

W258

L259

P260

I263

V264

N265

I266

V267

H268

V269

D272

I275

N284

N290

F293

N294

P295

L296

I297

Y298

C299

R300

S301

P302

D303

I306

A307

F308

L314

ARG

ARG

SER

SER

LEU

LYS

ALA

TYR

GLY

ASN

GLY

TYR

SER

SER

ASN

GLY

ASN

THR

GLY

GLU

GLN

SER

GLY

• Molecule 2: Lysozyme

Chain B:

GLY

N100

2I1

003

F100

4E1

005

I100

9D1

010

E101

1G1

012

L101

3R1

014

I101

7Y1

018

K101

9

Y102

5•

T102

6I1

027

G102

8I1

029

G103

0H1

031

L103

2L1

033•

T103

4

P103

7•

E104

5L1

046

D104

7

I105

0G1

051

R105

2N1

053

T105

4N1

055

G105

6V1

057

I105

8T1

059

K106

0D1

061

E106

2

K106

5L1

066

F106

7

D107

0V1

071

D107

2A1

073

A107

4V1

075

R107

6G1

077

I107

8L1

079

R108

0

K108

3•

L108

4K1

085

P108

6V1

087

Y108

8D1

089•

D109

2

R109

5R1

096

A109

7A1

098

L109

9I1

100

N110

1

F110

4Q1

105

S111

7L1

118

R111

9M1

120

L112

1

K112

4•

D112

7•

E112

8A1

129

W113

8Y1

139

R114

5A1

146

V114

9I1

150

Y116

1A1

162

A116

3

Page 6 Full wwPDB X-ray Structure Validation Report 4GBR

4 Data and refinement statistics i○

Property Value SourceSpace group P 21 21 21 DepositorCell constantsa, b, c, α, β, γ

51.38Å 71.38Å 161.37Å90.00◦ 90.00◦ 90.00◦ Depositor

Resolution (Å) 29.74 – 3.9929.74 – 3.99

DepositorEDS

% Data completeness(in resolution range)

90.8 (29.74-3.99)82.9 (29.74-3.99)

DepositorEDS

Rmerge (Not available) DepositorRsym (Not available) Depositor

< I/σ(I) > 1 1.56 (at 3.98Å) XtriageRefinement program PHENIX (phenix.refine: 1.7.3_928) Depositor

R, Rfree0.265 , 0.2820.273 , 0.312

DepositorDCC

Rfree test set 736 reflections (15.01%) wwPDB-VPWilson B-factor (Å2) 142.5 Xtriage

Anisotropy 0.495 XtriageBulk solvent ksol(e/Å3), Bsol(Å2) 0.28 , 149.7 EDS

L-test for twinning2 < |L| > = 0.48, < L2 > = 0.31 XtriageEstimated twinning fraction No twinning to report. Xtriage

Fo,Fc correlation 0.89 EDSTotal number of atoms 3610 wwPDB-VP

Average B, all atoms (Å2) 189.0 wwPDB-VP

Xtriage’s analysis on translational NCS is as follows: The largest off-origin peak in the Pattersonfunction is 5.77% of the height of the origin peak. No significant pseudotranslation is detected.

1Intensities estimated from amplitudes.2Theoretical values of < |L| >, < L2 > for acentric reflections are 0.5, 0.333 respectively for untwinned datasets,

and 0.375, 0.2 for perfectly twinned datasets.

Page 7 Full wwPDB X-ray Structure Validation Report 4GBR

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:CAU

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 0.25 0/2363 0.41 0/32202 B 0.22 0/1305 0.39 0/1760All All 0.24 0/3668 0.41 0/4980

There are no bond length outliers.

There are no bond angle outliers.

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 2303 0 2351 72 12 B 1285 0 1304 47 13 A 22 0 21 4 0All All 3610 0 3676 118 1

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 16.

All (118) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Page 8 Full wwPDB X-ray Structure Validation Report 4GBR

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

2:B:1013:LEU:HG 2:B:1029:ILE:HG12 1.59 0.831:A:284:ASN:HD21 3:A:500:CAU:H223 1.49 0.762:B:1050:ILE:HG22 2:B:1051:GLY:H 1.50 0.762:B:1105:GLN:OE1 2:B:1138:TRP:NE1 2.19 0.721:A:230:LEU:HB3 1:A:241:HIS:CE1 2.25 0.711:A:284:ASN:ND2 3:A:500:CAU:H223 2.06 0.701:A:232:LYS:HG3 1:A:233:ILE:H 1.56 0.681:A:188:GLU:OE2 2:B:1013:LEU:HD22 1.95 0.681:A:255:THR:O 1:A:259:LEU:HB2 1.95 0.67

1:A:167:LEU:HB2 1:A:168:PRO:HD3 1.77 0.672:B:1050:ILE:HG22 2:B:1051:GLY:N 2.10 0.672:B:1105:GLN:HB2 2:B:1145:ARG:CZ 2.26 0.651:A:232:LYS:HG3 1:A:233:ILE:N 2.13 0.64

2:B:1087:VAL:HG21 2:B:1118:LEU:HB3 1.79 0.642:B:1096:ARG:O 2:B:1100:ILE:HG13 2.00 0.61

1:A:284:ASN:HD21 3:A:500:CAU:C22 2.12 0.611:A:230:LEU:HB3 1:A:241:HIS:HE1 1.65 0.611:A:230:LEU:HD12 1:A:231:GLN:N 2.17 0.591:A:232:LYS:CG 1:A:233:ILE:H 2.15 0.581:A:245:LYS:O 1:A:249:ILE:HG13 2.04 0.58

2:B:1120:MET:HE3 2:B:1129:ALA:HA 1.84 0.581:A:38:ILE:O 1:A:42:LEU:HG 2.03 0.581:A:148:ASN:O 1:A:152:VAL:HG23 2.04 0.572:B:1046:LEU:O 2:B:1050:ILE:HG12 2.05 0.56

2:B:1105:GLN:HB2 2:B:1145:ARG:NH2 2.21 0.551:A:122:GLU:O 1:A:126:VAL:HG23 2.07 0.55

1:A:264:VAL:HG13 1:A:275:ILE:HD12 1.88 0.551:A:68:THR:O 1:A:72:ILE:HG12 2.07 0.55

2:B:1085:LYS:HB3 2:B:1086:PRO:HD3 1.89 0.541:A:64:LEU:HD21 1:A:303:ASP:HB3 1.91 0.532:B:1033:LEU:HD21 2:B:1046:LEU:HD13 1.91 0.53

1:A:174:TYR:O 1:A:196:ASN:ND2 2.42 0.532:B:1105:GLN:HB2 2:B:1145:ARG:NH1 2.24 0.522:B:1031:HIS:ND1 2:B:1070:ASP:OD2 2.40 0.522:B:1061:ASP:O 2:B:1065:LYS:HG2 2.10 0.52

2:B:1138:TRP:CH2 2:B:1146:ALA:HA 2.44 0.521:A:91:ALA:O 1:A:95:LEU:HG 2.10 0.522:B:1005:GLU:O 2:B:1009:ILE:HG13 2.10 0.521:A:265:ASN:O 1:A:269:VAL:HG23 2.10 0.52

2:B:1034:THR:HB 2:B:1045:GLU:HG3 1.90 0.522:B:1004:PHE:HD1 2:B:1067:PHE:CE2 2.28 0.521:A:207:SER:HB2 3:A:500:CAU:H10 1.92 0.51

Continued on next page...

Page 9 Full wwPDB X-ray Structure Validation Report 4GBR

Continued from previous page...

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:A:249:ILE:HG22 1:A:297:ILE:HD13 1.92 0.512:B:1092:ASP:OD2 2:B:1095:ARG:NH1 2.40 0.511:A:293:PHE:O 1:A:297:ILE:HG13 2.10 0.511:A:229:GLN:O 1:A:232:LYS:N 2.39 0.51

1:A:259:LEU:HB3 1:A:260:PRO:HD3 1.93 0.511:A:40:MET:HA 1:A:43:ILE:HD12 1.91 0.511:A:141:TYR:OH 1:A:241:HIS:NE2 2.43 0.511:A:232:LYS:CG 1:A:233:ILE:N 2.74 0.501:A:218:VAL:O 1:A:222:VAL:HG23 2.11 0.501:A:140:LYS:O 1:A:141:TYR:HB2 2.12 0.49

2:B:1026:THR:HG23 2:B:1031:HIS:O 2.12 0.491:A:260:PRO:O 1:A:264:VAL:HG23 2.13 0.491:A:34:VAL:O 1:A:38:ILE:HG12 2.11 0.49

1:A:111:SER:HA 1:A:169:ILE:HD12 1.94 0.491:A:39:VAL:O 1:A:43:ILE:HG13 2.13 0.49

2:B:1027:ILE:HG12 2:B:1028:GLY:N 2.28 0.491:A:66:THR:O 1:A:70:TYR:HD1 1.96 0.482:B:1098:ALA:O 2:B:1101:ASN:HB3 2.14 0.482:B:1139:TYR:HA 2:B:1146:ALA:CB 2.44 0.482:B:1145:ARG:O 2:B:1149:VAL:HG23 2.14 0.471:A:294:ASN:HB2 1:A:295:PRO:HD3 1.95 0.471:A:131:ARG:NE 1:A:131:ARG:HA 2.29 0.471:A:141:TYR:CE2 1:A:236:PHE:HB3 2.50 0.472:B:1050:ILE:CG2 2:B:1051:GLY:H 2.25 0.472:B:1047:ASP:OD1 2:B:1053:ASN:HA 2.15 0.471:A:250:ILE:HD13 1:A:297:ILE:HD12 1.96 0.471:A:268:HIS:NE2 1:A:275:ILE:HB 2.31 0.461:A:86:VAL:HA 1:A:109:TRP:HE1 1.81 0.46

1:A:135:ILE:HD13 1:A:225:GLU:HB3 1.98 0.461:A:36:MET:CG 1:A:95:LEU:HD21 2.46 0.462:B:1067:PHE:O 2:B:1071:VAL:HG23 2.15 0.461:A:268:HIS:HB3 1:A:272:ASP:OD1 2.16 0.451:A:108:PHE:O 1:A:112:ILE:HG13 2.16 0.45

2:B:1033:LEU:HD22 2:B:1046:LEU:HB2 1.98 0.451:A:35:GLY:O 1:A:39:VAL:HG23 2.17 0.451:A:220:SER:O 1:A:224:GLN:HG3 2.17 0.451:A:225:GLU:CD 1:A:228:ARG:HH21 2.21 0.45

2:B:1014:ARG:HD3 2:B:1018:TYR:CE2 2.52 0.452:B:1050:ILE:CG2 2:B:1051:GLY:N 2.80 0.452:B:1120:MET:HB2 2:B:1120:MET:HE2 1.82 0.451:A:140:LYS:HD3 1:A:229:GLN:NE2 2.32 0.44

Continued on next page...

Page 10 Full wwPDB X-ray Structure Validation Report 4GBR

Continued from previous page...

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:A:141:TYR:CZ 1:A:236:PHE:HB3 2.52 0.442:B:1071:VAL:O 2:B:1075:VAL:HG23 2.17 0.442:B:1019:LYS:HE2 2:B:1025:TYR:CZ 2.52 0.442:B:1010:ASP:OD1 2:B:1161:TYR:HE1 2.01 0.44

1:A:77:CYS:O 1:A:81:VAL:HG23 2.17 0.442:B:1146:ALA:O 2:B:1150:ILE:HG13 2.18 0.441:A:252:GLY:O 1:A:256:LEU:HG 2.18 0.43

2:B:1059:THR:OG1 2:B:1062:GLU:HG3 2.18 0.432:B:1003:ILE:HG23 2:B:1004:PHE:N 2.34 0.431:A:302:PRO:O 1:A:306:ILE:HG13 2.19 0.431:A:172:HIS:HB3 1:A:175:ARG:HG3 2.02 0.421:A:184:CYS:SG 1:A:192:ASP:HB2 2.58 0.421:A:257:CYS:SG 1:A:290:ASN:HB2 2.59 0.421:A:40:MET:O 1:A:44:VAL:HG23 2.18 0.421:A:153:ILE:O 1:A:157:VAL:HG23 2.19 0.422:B:1012:GLY:O 2:B:1029:ILE:HG23 2.20 0.421:A:53:LEU:HG 1:A:308:PHE:CE1 2.55 0.42

2:B:1027:ILE:HG12 2:B:1028:GLY:H 1.84 0.421:A:245:LYS:HD3 1:A:300:ARG:HH22 1.84 0.421:A:210:VAL:N 1:A:211:PRO:HD2 2.35 0.422:B:1117:SER:O 2:B:1121:LEU:HG 2.20 0.421:A:227:LYS:HA 1:A:230:LEU:HG 2.01 0.411:A:259:LEU:O 1:A:263:ILE:HG13 2.21 0.41

1:A:234:ASP:HB3 1:A:235:LYS:HB3 2.02 0.411:A:237:CYS:SG 1:A:240:GLU:HG2 2.61 0.411:A:263:ILE:O 1:A:267:VAL:HG23 2.20 0.41

2:B:1076:ARG:HB3 2:B:1080:ARG:HH12 1.85 0.411:A:36:MET:HG2 1:A:95:LEU:HD21 2.03 0.40

2:B:1054:THR:HG21 2:B:1058:ILE:HG22 2.03 0.402:B:1076:ARG:HB3 2:B:1080:ARG:NH1 2.36 0.401:A:29:ASP:HB2 1:A:32:TRP:HB3 2.04 0.40

2:B:1017:ILE:HG13 2:B:1056:GLY:O 2.21 0.401:A:149:LYS:O 1:A:153:ILE:HG12 2.22 0.40

1:A:72:ILE:HG23 1:A:298:TYR:CZ 2.57 0.402:B:1074:ALA:O 2:B:1078:ILE:HG13 2.22 0.40

All (1) symmetry-related close contacts are listed below. The label for Atom-2 includes the sym-metry operator and encoded unit-cell translations to be applied.

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:A:235:LYS:NZ 2:B:1072:ASP:OD1[3_555] 2.09 0.11

Page 11 Full wwPDB X-ray Structure Validation Report 4GBR

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 X-ray entries followed by that with respect to entriesof similar resolution.

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 284/309 (92%) 278 (98%) 6 (2%) 0 100 100

2 B 160/163 (98%) 149 (93%) 11 (7%) 0 100 100

All All 444/472 (94%) 427 (96%) 17 (4%) 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 chain as apercentile score with respect to all X-ray entries followed by that with respect to entries of similarresolution.

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 254/271 (94%) 252 (99%) 2 (1%) 83 92

2 B 133/133 (100%) 131 (98%) 2 (2%) 67 84

All All 387/404 (96%) 383 (99%) 4 (1%) 78 89

All (4) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 A 143 SER1 A 223 PHE2 B 1013 LEU2 B 1104 PHE

Some sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (4) suchsidechains are listed below:

Page 12 Full wwPDB X-ray Structure Validation Report 4GBR

Mol Chain Res Type1 A 229 GLN1 A 284 ASN2 B 1068 ASN2 B 1132 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.

5.5 Carbohydrates i○

There are no carbohydrates in this entry.

5.6 Ligand geometry i○

1 ligand is 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

3 CAU A 500 - 22,24,24 1.33 3 (13%) 32,33,33 1.67 7 (21%)

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 Rings3 CAU A 500 - - 0/10/10/10 0/3/3/3

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All (3) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)3 A 500 CAU O17-C16 -2.36 1.36 1.433 A 500 CAU C1-C2 2.14 1.41 1.363 A 500 CAU C11-C10 2.33 1.42 1.36

All (7) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)3 A 500 CAU C6-C5-C4 -2.30 116.86 120.833 A 500 CAU C12-C13-C9 -2.09 119.04 121.543 A 500 CAU C1-C2-C3 -2.03 117.07 120.083 A 500 CAU O14-C13-C9 2.13 120.14 117.113 A 500 CAU C5-C4-C3 2.91 122.02 118.173 A 500 CAU O14-C15-C16 4.40 116.20 107.673 A 500 CAU C18-C16-C15 4.50 117.72 110.47

There are no chirality outliers.

There are no torsion outliers.

There are no ring outliers.

1 monomer is involved in 4 short contacts:

Mol Chain Res Type Clashes Symm-Clashes3 A 500 CAU 4 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.

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6 Fit of model and data i○

6.1 Protein, DNA and RNA chains i○

In the following table, the column labelled ‘#RSRZ> 2’ contains the number (and percentage)of RSRZ outliers, followed by percent RSRZ outliers for the chain as percentile scores relative toall X-ray entries and entries of similar resolution. The OWAB column contains the minimum,median, 95th percentile and maximum values of the occupancy-weighted average B-factor perresidue. The column labelled ‘Q< 0.9’ lists the number of (and percentage) of residues with anaverage occupancy less than 0.9.

Mol Chain Analysed <RSRZ> #RSRZ>2 OWAB(Å2) Q<0.9

1 A 286/309 (92%) 0.06 10 (3%) 44 33 110, 184, 267, 302 0

2 B 162/163 (99%) 0.17 7 (4%) 35 26 125, 175, 235, 249 0

All All 448/472 (94%) 0.10 17 (3%) 40 30 110, 181, 264, 302 0

All (17) RSRZ outliers are listed below:

Mol Chain Res Type RSRZ1 A 142 GLN 7.91 A 141 TYR 4.11 A 146 THR 3.42 B 1037 PRO 3.41 A 145 LEU 3.42 B 1089 ASP 2.91 A 140 LYS 2.71 A 143 SER 2.62 B 1025 TYR 2.52 B 1127 ASP 2.41 A 192 ASP 2.31 A 135 ILE 2.32 B 1083 LYS 2.21 A 171 MET 2.22 B 1033 LEU 2.22 B 1124 LYS 2.11 A 188 GLU 2.1

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

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

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6.3 Carbohydrates i○

There are no carbohydrates in this entry.

6.4 Ligands i○

In the following table, the Atoms column lists the number of modelled atoms in the group and thenumber defined in the chemical component dictionary. The B-factors column lists the minimum,median, 95th percentile and maximum values of B factors of atoms in the group. The columnlabelled ‘Q< 0.9’ lists the number of atoms with occupancy less than 0.9.

Mol Type Chain Res Atoms RSCC RSR B-factors(Å2) Q<0.93 CAU A 500 22/22 0.91 0.25 158,160,163,164 0

6.5 Other polymers i○

There are no such residues in this entry.