wwPDB X-ray Structure Validation Summary Report i · wwPDB X-ray Structure Validation Summary Report i Mar8,2018–05:12pmGMT PDBID : 3NVV ... Q62 I66 L74 A75 P76 E89 R104 Q131 P132

wwPDB X-ray Structure Validation Summary Report i○

Mar 8, 2018 – 05:12 pm GMT

PDB ID : 3NVVTitle : Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite

Authors : Cao, H.; Hille, R.Deposited on : 2010-07-08

Resolution : 1.82 Å(reported)

This is a wwPDB X-ray Structure Validation Summary 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/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

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



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

Page 2 wwPDB X-ray Structure Validation Summary Report 3NVV

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 1.82 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 6455 (1.84-1.80)Clashscore 122126 7349 (1.84-1.80)

Ramachandran outliers 120053 7272 (1.84-1.80)Sidechain outliers 120020 7272 (1.84-1.80)RSRZ outliers 108989 6347 (1.84-1.80)

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 164

1 J 164

2 B 334

2 K 334

3 C 755

3 L 755

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


2 Entry composition i○

There are 9 unique types of molecules in this entry. The entry contains 20671 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 Xanthine dehydrogenase/oxidase.

Mol Chain Residues Atoms ZeroOcc AltConf Trace

1 A 164 Total C N O S1255 788 225 230 12 0 0 0

1 J 164 Total C N O S1255 788 225 230 12 0 0 0



2 B 334 Total C N O S2630 1700 437 479 14 0 0 0

2 K 305 Total C N O S2389 1539 402 435 13 0 0 0



3 C 755 Total C N O S5823 3680 1003 1105 35 0 0 0

3 L 745 Total C N O S5761 3643 992 1093 33 0 0 0

• Molecule 4 is FE2/S2 (INORGANIC) CLUSTER (three-letter code: FES) (formula: Fe2S2).

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


Mol Chain Residues Atoms ZeroOcc AltConf

4 A 1 Total Fe S4 2 2 0 0

4 A 1 Total Fe S4 2 2 0 0

4 J 1 Total Fe S4 2 2 0 0

4 J 1 Total Fe S4 2 2 0 0

• Molecule 5 is FLAVIN-ADENINE DINUCLEOTIDE (three-letter code: FAD) (formula:C27H33N9O15P2).



5 B 1 Total C N O P53 27 9 15 2 0 0

5 K 1 Total C N O P53 27 9 15 2 0 0

• Molecule 6 is PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER (three-letter code: MTE) (formula: C10H14N5O6PS2).


6 C 1 Total C N O P S24 10 5 6 1 2 0 0

6 L 1 Total C N O P S24 10 5 6 1 2 0 0

• Molecule 7 is DIOXOTHIOMOLYBDENUM(VI) ION (three-letter code: MOS) (formula:HMoO2S).



7 C 1 Total Mo O S4 1 2 1 0 0

7 L 1 Total Mo O S4 1 2 1 0 0

• Molecule 8 is ARSENITE (three-letter code: AST) (formula: AsO3).


8 C 1 Total As O3 1 2 0 0

8 L 1 Total As O3 1 2 0 0


• Molecule 9 is water.


9 A 94 Total O94 94 0 0

9 B 137 Total O137 137 0 0

9 C 465 Total O465 465 0 0

9 J 99 Total O99 99 0 0

9 K 105 Total O105 105 0 0

9 L 474 Total O474 474 0 0


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: Xanthine dehydrogenase/oxidase

Chain A:

T2•

L36

R37

G42

C43

K57

Y58

D59

R60•

L61•

I66

H82

E89

S93

Y125

R129

N130

Q131

P132

E133

E140

K165


Chain J:

T2 Y29

K33

L36

R37

G42

C43

G44

E45

K57

Y58•

D59

R60•

L61•

Q62

I66

L74

A75

P76

E89

R104

Q131

P132

E133•

P134

F143

Q144

G159

F160

R161•

T162

F163

A164

K165


Chain B:

L195

F196

N197

E200

T207•

I211•

L217

K220

P223

P224

T241

L242

K243

L248•

K249

K256

I264

M268

N272•

F275

P281

P285

E286

L287

L312

W336•

F337

A338•

G339

A346

G378•

L398

E401

L405

A424•

S425•

R426

R427

K433

R439

V440

L441

E451

K468•

E480

E506

G528


Chain K:

LEU

PHE

ASN

PRO

GLU

GLU

PHE

MET

PRO

LEU

ASP

PRO

THR

GLN

GLU

PRO

ILE

PHE

PRO

PRO

GLU

LEU

LEU

ARG

LEU

LYS

ASP

VAL

PRO

P224

E232

T241

L242

K243•

E254•

A255

K256

L257

E263

N272•

F275

P281

L287

E295•

A301

V308

L312

L313

E314•

R328

R335•

W336•

F337

A346

S347

L348

R377

G378•

T379•

F389

R394

K395

T396

L397

L398

E414•

A424•

S425•

R426•

D429•

K433

R439

V440•

M447

E451

L467•

L474•

S475•

K476

F477•

C487

M504

L513

L527

G528•


Chain C:

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


D571

T572

R575

D595

R598

Y599

E600

N601

T609

H614

E624

I640

P641

F655

G664

V670

D673

H677

A681

V684

P693

A694

I695

D700

N705

L719

F742

Y743

H747

I752

E759

F763

M779

V782

P783

R786

G797

L814

H821

R829

T836

H840

A844

V848

T853

S874

R880

H884

M885

R895

G896

N904

F911

R912

G913

F914

I922

A923

E924

N925

W926

E939

R942

W943

K944

R958

K995

G100

6I1

007

S100

8

H103

3G1

034

G103

5

Q104

8

A107

9S1

080

V108

1

Q109

5

K109

9

K110

5

W111

6

D112

3

G113

9

G118

3

N118

7

L120

3

L120

8

C124

7P1

248

N124

9

A125

5

E126

1P1

262

Q128

4

N128

7

C132

5•


Chain L:

D571

R575

R598

Y599

E600

N601

R606

T609

H614

S623

Q626

F655

T659

V670

D673

H677

A681

V684

V685

K686

P693

A694

I695

I696

T697

I698

E699

E711

L719

K720

E725

H741

F742

Y743

H747

S774

V782

G797

L814

K818

H821

R829

D832

I835

H840

T853

I856

E860

S874

R880

H884

R895

R899

N904

F911

R912

G913

F914

A923

W926

M927

E939

K944

L952

R958•

Y977

R980

K995

G100

6I1

007

S100

8

L102

0I1

021

V103

1S1

032

H103

3G1

034

G103

5

Q104

8

Y106

2

Q108

8

Q109

5

K109

9

K110

7

Y113

3

G113

9

R117

5

N118

7

L120

3

P122

4

F123

2

E123

8

N124

9

A125

5S1

256

K125

7

E126

1P1

262

R128

2A1

283

Q128

4H1

285

T128

6N1

287•

N128

8•

N128

9•

T129

0•

K129

1E1

292

V131

0

T131

5LE

UCY

SVA

LTH

RGL

YAL

APR

OGL

YAS

NCY

S


4 Data and refinement statistics i○

Property Value SourceSpace group P 1 21 1 DepositorCell constantsa, b, c, α, β, γ

132.77Å 73.42Å 138.16Å90.00◦ 96.93◦ 90.00◦ Depositor

Resolution (Å) 131.80 – 1.82131.80 – 1.82

DepositorEDS

% Data completeness(in resolution range)

97.2 (131.80-1.82)97.2 (131.80-1.82)

DepositorEDS

Rmerge (Not available) DepositorRsym (Not available) Depositor

< I/σ(I) > 1 2.18 (at 1.82Å) XtriageRefinement program REFMAC 5.2.0019 Depositor

R, Rfree0.193 , 0.2290.193 , 0.230

DepositorDCC

Rfree test set 11464 reflections (5.01%) wwPDB-VPWilson B-factor (Å2) 20.2 Xtriage

Anisotropy 0.081 XtriageBulk solvent ksol(e/Å3), Bsol(Å2) 0.38 , 55.7 EDS

L-test for twinning2 < |L| > = 0.47, < L2 > = 0.30 XtriageEstimated twinning fraction 0.016 for l,-k,h Xtriage

Fo,Fc correlation 0.95 EDSTotal number of atoms 20671 wwPDB-VP

Average B, all atoms (Å2) 24.0 wwPDB-VP

Xtriage’s analysis on translational NCS is as follows: The largest off-origin peak in the Pattersonfunction is 2.91% 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.

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#data_stats


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:MOS, MTE, FES, FAD, AST

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 0.62 0/1277 0.67 0/17231 J 0.57 0/1277 0.64 0/17232 B 0.49 0/2689 0.60 2/3637 (0.1%)2 K 0.47 0/2438 0.59 1/3290 (0.0%)3 C 0.63 0/5951 0.69 5/8061 (0.1%)3 L 0.58 0/5888 0.67 5/7974 (0.1%)All All 0.57 0/19520 0.66 13/26408 (0.0%)

There are no bond length outliers.

The worst 5 of 13 bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)3 C 829 ARG NE-CZ-NH2 -10.72 114.94 120.303 C 829 ARG NE-CZ-NH1 8.37 124.48 120.303 L 829 ARG NE-CZ-NH2 -7.93 116.33 120.303 C 1203 LEU CA-CB-CG 7.90 133.47 115.303 L 829 ARG NE-CZ-NH1 7.46 124.03 120.30

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.

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

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

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


Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes1 A 1255 0 1265 11 01 J 1255 0 1265 20 02 B 2630 0 2697 18 02 K 2389 0 2459 23 03 C 5823 0 5744 74 13 L 5761 0 5685 66 04 A 8 0 0 0 04 J 8 0 0 0 05 B 53 0 31 1 05 K 53 0 31 3 06 C 24 0 10 0 06 L 24 0 10 0 07 C 4 0 0 1 07 L 4 0 0 1 08 C 3 0 0 1 08 L 3 0 0 1 09 A 94 0 0 0 09 B 137 0 0 3 09 C 465 0 0 4 09 J 99 0 0 1 09 K 105 0 0 1 09 L 474 0 0 3 1All All 20671 0 19197 200 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 5.

The worst 5 of 200 close contacts within the same asymmetric unit are listed below, sorted bytheir clash magnitude.

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

2:K:243:LYS:HD3 2:K:243:LYS:H 1.05 1.123:C:641:PRO:HD2 3:C:779:MET:CE 1.84 1.062:K:243:LYS:HD3 2:K:243:LYS:N 1.75 0.993:C:641:PRO:HD2 3:C:779:MET:HE1 1.44 0.993:C:924:GLU:OE1 3:C:942:ARG:NH1 1.97 0.96

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)

3:C:958:ARG:NH2 9:L:1506:HOH:O[2_655] 1.88 0.32


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 162/164 (99%) 158 (98%) 4 (2%) 0 100 100

1 J 162/164 (99%) 157 (97%) 4 (2%) 1 (1%) 27 13

2 B 332/334 (99%) 317 (96%) 15 (4%) 0 100 100

2 K 303/334 (91%) 290 (96%) 13 (4%) 0 100 100

3 C 753/755 (100%) 736 (98%) 13 (2%) 4 (0%) 31 16

3 L 743/755 (98%) 722 (97%) 17 (2%) 4 (0%) 31 16

All All 2455/2506 (98%) 2380 (97%) 66 (3%) 9 (0%) 36 22

5 of 9 Ramachandran outliers are listed below:

Mol Chain Res Type3 C 1008 SER3 L 1008 SER3 C 912 ARG3 L 912 ARG3 L 1139 GLY

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 137/137 (100%) 132 (96%) 5 (4%) 38 21

1 J 137/137 (100%) 136 (99%) 1 (1%) 85 82

2 B 290/290 (100%) 284 (98%) 6 (2%) 56 44Continued on next page...

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

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

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


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

2 K 261/290 (90%) 252 (97%) 9 (3%) 40 24

3 C 631/631 (100%) 620 (98%) 11 (2%) 63 53

3 L 624/631 (99%) 608 (97%) 16 (3%) 49 34

All All 2080/2116 (98%) 2032 (98%) 48 (2%) 53 39

5 of 48 residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type3 C 1287 ASN2 K 337 PHE3 L 939 GLU1 J 165 LYS2 K 312 LEU

Some sidechains can be flipped to improve hydrogen bonding and reduce clashes. 5 of 40 suchsidechains are listed below:

Mol Chain Res Type3 C 1287 ASN1 J 146 ASN3 L 1048 GLN1 J 131 GLN2 K 292 HIS

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.

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

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



5.6 Ligand geometry i○

12 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).

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

4 FES A 601 1 0,4,4 0.00 - 0,4,4 0.00 -4 FES A 602 1 0,4,4 0.00 - 0,4,4 0.00 -5 FAD B 606 - 51,58,58 1.35 6 (11%) 57,89,89 2.20 7 (12%)8 AST C 1 - 0,2,3 0.00 - 0,1,3 0.00 -6 MTE C 1326 7 21,26,26 1.58 3 (14%) 19,40,40 2.15 9 (47%)7 MOS C 1327 6 0,3,3 0.00 - 0,3,3 0.00 -4 FES J 601 1 0,4,4 0.00 - 0,4,4 0.00 -4 FES J 602 1 0,4,4 0.00 - 0,4,4 0.00 -5 FAD K 606 - 51,58,58 1.36 6 (11%) 57,89,89 1.94 8 (14%)8 AST L 1 - 0,2,3 0.00 - 0,1,3 0.00 -6 MTE L 1326 7 21,26,26 1.59 2 (9%) 19,40,40 1.96 4 (21%)7 MOS L 1327 6 0,3,3 0.00 - 0,3,3 0.00 -

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 FES A 601 1 - 0/0/4/4 0/1/1/14 FES A 602 1 - 0/0/4/4 0/1/1/15 FAD B 606 - - 0/28/50/50 0/6/6/68 AST C 1 - - 0/0/0/0 0/0/0/06 MTE C 1326 7 - 0/6/34/34 0/3/3/37 MOS C 1327 6 - 0/0/0/0 0/0/0/04 FES J 601 1 - 0/0/4/4 0/1/1/14 FES J 602 1 - 0/0/4/4 0/1/1/15 FAD K 606 - - 0/28/50/50 0/6/6/68 AST L 1 - - 0/0/0/0 0/0/0/06 MTE L 1326 7 - 0/6/34/34 0/3/3/37 MOS L 1327 6 - 0/0/0/0 0/0/0/0



The worst 5 of 17 bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)6 C 1326 MTE C4-N3 2.11 1.36 1.335 B 606 FAD C2A-N1A 2.26 1.38 1.335 K 606 FAD C5X-N5 2.36 1.38 1.355 B 606 FAD C4-N3 2.46 1.37 1.335 K 606 FAD C2A-N1A 2.67 1.38 1.33

The worst 5 of 28 bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)5 B 606 FAD N3A-C2A-N1A -11.79 118.78 128.865 K 606 FAD N3A-C2A-N1A -9.87 120.42 128.866 C 1326 MTE O3’-C7-C6 -3.90 106.36 108.966 C 1326 MTE O2P-P-O4’ -3.03 98.67 106.735 K 606 FAD O3’-C3’-C2’ -2.76 102.00 108.82

There are no chirality outliers.

There are no torsion outliers.

There are no ring outliers.

6 monomers are involved in 8 short contacts:

Mol Chain Res Type Clashes Symm-Clashes5 B 606 FAD 1 08 C 1 AST 1 07 C 1327 MOS 1 05 K 606 FAD 3 08 L 1 AST 1 07 L 1327 MOS 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/XrayValidationReportHelp#polymer_linkage


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 164/164 (100%) -0.06 3 (1%) 68 64 10, 20, 34, 43 0

1 J 164/164 (100%) -0.03 5 (3%) 50 45 13, 22, 42, 52 0

2 B 334/334 (100%) 0.26 10 (2%) 50 45 17, 29, 42, 50 0

2 K 305/334 (91%) 0.38 20 (6%) 18 14 21, 33, 45, 49 0

3 C 755/755 (100%) -0.22 1 (0%) 95 93 11, 18, 28, 35 0

3 L 745/755 (98%) -0.16 5 (0%) 87 86 12, 20, 34, 60 0

All All 2467/2506 (98%) -0.04 44 (1%) 68 64 10, 22, 40, 60 0

The worst 5 of 44 RSRZ outliers are listed below:

Mol Chain Res Type RSRZ3 L 1290 THR 7.31 J 61 LEU 6.13 L 1288 ASN 6.11 J 58 TYR 6.11 A 61 LEU 6.0

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

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

6.3 Carbohydrates i○

There are no carbohydrates in this entry.

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#fit_model_data

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#fit_protein_na_chains

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#fit_nonstandard_and_ligands



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<0.95 FAD B 606 53/53 0.96 0.10 17,21,27,29 05 FAD K 606 53/53 0.97 0.09 20,26,28,30 06 MTE L 1326 24/24 0.98 0.08 12,14,19,21 06 MTE C 1326 24/24 0.98 0.09 9,12,17,19 04 FES J 601 4/4 0.99 0.08 14,14,16,16 08 AST C 1 3/4 0.99 0.08 21,21,22,23 07 MOS L 1327 4/4 0.99 0.10 12,19,19,29 04 FES J 602 4/4 0.99 0.09 15,15,16,16 07 MOS C 1327 4/4 0.99 0.11 18,20,24,32 08 AST L 1 3/4 0.99 0.09 26,26,26,31 04 FES A 602 4/4 0.99 0.09 14,15,16,16 04 FES A 601 4/4 1.00 0.10 13,14,14,15 0

6.5 Other polymers i○

There are no such residues in this entry.



Documents

wwPDB X-ray Structure Validation Summary Report i · wwPDB X-ray Structure Validation Summary Report i Mar8,2018–05:12pmGMT PDBID : 3NVV ... Q62 I66 L74 A75 P76 E89 R104 Q131 P132