Post on 29-Dec-2019
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 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 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
Page 3 wwPDB X-ray Structure Validation Summary Report 3NVV
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
• Molecule 2 is a protein called Xanthine dehydrogenase/oxidase.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
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
• Molecule 3 is a protein called Xanthine dehydrogenase/oxidase.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
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).
Page 4 wwPDB X-ray Structure Validation Summary Report 3NVV
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).
Page 5 wwPDB X-ray Structure Validation Summary Report 3NVV
Mol Chain Residues Atoms ZeroOcc AltConf
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).
Mol Chain Residues Atoms ZeroOcc AltConf
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).
Page 6 wwPDB X-ray Structure Validation Summary Report 3NVV
Mol Chain Residues Atoms ZeroOcc AltConf
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).
Mol Chain Residues Atoms ZeroOcc AltConf
8 C 1 Total As O3 1 2 0 0
8 L 1 Total As O3 1 2 0 0
Page 7 wwPDB X-ray Structure Validation Summary Report 3NVV
• Molecule 9 is water.
Mol Chain Residues Atoms ZeroOcc AltConf
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
Page 8 wwPDB X-ray Structure Validation Summary Report 3NVV
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
• Molecule 1: Xanthine dehydrogenase/oxidase
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
• Molecule 2: Xanthine dehydrogenase/oxidase
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
• Molecule 2: Xanthine dehydrogenase/oxidase
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•
• Molecule 3: Xanthine dehydrogenase/oxidase
Chain C:
Page 9 wwPDB X-ray Structure Validation Summary Report 3NVV
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•
• Molecule 3: Xanthine dehydrogenase/oxidase
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
Page 10 wwPDB X-ray Structure Validation Summary Report 3NVV
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.
Page 11 wwPDB X-ray Structure Validation Summary Report 3NVV
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.
Page 12 wwPDB X-ray Structure Validation Summary Report 3NVV
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
Page 13 wwPDB X-ray Structure Validation Summary Report 3NVV
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...
Page 14 wwPDB X-ray Structure Validation Summary Report 3NVV
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.
Page 15 wwPDB X-ray Structure Validation Summary Report 3NVV
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
Page 16 wwPDB X-ray Structure Validation Summary Report 3NVV
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.
Page 17 wwPDB X-ray Structure Validation Summary Report 3NVV
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.
Page 18 wwPDB X-ray Structure Validation Summary Report 3NVV
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.