Full wwPDB X-ray Structure Validation Report O i · 2020. 5. 31. · Stretches of 2 or more consecutive residues without any outlier are shown as a green connector. Residues present

Full wwPDB X-ray Structure Validation Report iO

May 15, 2020 � 09:50 am BST

PDB ID : 5MZCTitle : Pseudomonas �uorescens kynurenine 3-monooxygenase (KMO) in complex

with 3-(5-chloro-6-ethoxy-2-oxo-2,3-dihydro-1,3-benzoxazol-3-yl)propanoic acid

Authors : Rowland, P.Deposited on : 2017-01-31Resolution : 1.82 Å(reported)

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

We welcome your comments at [email protected]

A user guide is available athttps://www.wwpdb.org/validation/2017/XrayValidationReportHelp

with speci�c help available everywhere you see the iO symbol.

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

MolProbity : 4.02b-467Mogul : 1.8.5 (274361), CSD as541be (2020)

Xtriage (Phenix) : 1.13EDS : 2.11

buster-report : 1.1.7 (2018)Percentile statistics : 20191225.v01 (using entries in the PDB archive December 25th 2019)

Refmac : 5.8.0158CCP4 : 7.0.044 (Gargrove)

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

Validation Pipeline (wwPDB-VP) : 2.11

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



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

Page 2 Full wwPDB X-ray Structure Validation Report 5MZC

1 Overall quality at a glance iO

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.

MetricWhole archive(#Entries)

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

Rfree 130704 7484 (1.84-1.80)Clashscore 141614 8401 (1.84-1.80)

Ramachandran outliers 138981 8290 (1.84-1.80)Sidechain outliers 138945 8290 (1.84-1.80)RSRZ outliers 127900 7371 (1.84-1.80)

The table below summarises the geometric issues observed across the polymeric chains and their�t to the electron density. The red, orange, yellow and green segments on the lower bar indicatethe fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric qualitycriteria respectively. A grey segment represents the fraction of residues that are not modelled.The numeric value for each fraction is indicated below the corresponding segment, with a dotrepresenting fractions <=5% The upper red bar (where present) indicates the fraction of residuesthat have poor �t to the electron density. The numeric value is given above the bar.

Mol Chain Length Quality of chain

1 A 461

1 B 461

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


2 Entry composition iO

There are 6 unique types of molecules in this entry. The entry contains 7917 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 Kynurenine 3-monooxygenase.

Mol Chain Residues Atoms ZeroOcc AltConf Trace

1 A 448Total C N O S3482 2181 644 640 17

0 3 0

1 B 451Total C N O S3497 2191 647 641 18

0 2 0

There are 4 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceA 252 SER CYS con�ict UNP Q84HF5A 461 SER CYS con�ict UNP Q84HF5B 252 SER CYS con�ict UNP Q84HF5B 461 SER CYS con�ict UNP Q84HF5

� Molecule 2 is FLAVIN-ADENINE DINUCLEOTIDE (three-letter code: FAD) (formula:C27H33N9O15P2).

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


Mol Chain Residues Atoms ZeroOcc AltConf

2 A 1Total C N O P53 27 9 15 2

0 0

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

0 0

� Molecule 3 is CHLORIDE ION (three-letter code: CL) (formula: Cl).


3 B 1Total Cl1 1

0 0

3 A 1Total Cl1 1

0 0

� Molecule 4 is 3-(5-chloranyl-6-ethoxy-2-oxidanylidene-1,3-benzoxazol-3-yl)propanoic acid(three-letter code: 8EQ) (formula: C12H12ClNO5).


4 A 1Total C Cl N O19 12 1 1 5

0 0

4 A 1Total C Cl N O19 12 1 1 5

0 0

4 A 1Total C Cl N O19 12 1 1 5

0 0

4 B 1Total C Cl N O19 12 1 1 5

0 0

4 B 1Total C Cl N O19 12 1 1 5

0 0


� Molecule 5 is GLYCEROL (three-letter code: GOL) (formula: C3H8O3).


5 A 1Total C O6 3 3

0 0

5 B 1Total C O6 3 3

0 0

� Molecule 6 is water.


6 A 393Total O393 393

0 0

6 B 330Total O330 330

0 0


3 Residue-property plots iO

These plots are drawn for all protein, RNA and DNA chains in the entry. The �rst 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 geometry and 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 �t 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: Kynurenine 3-monooxygenase

Chain A:

MET

THR

ALA

THR

ASP

ASN

A7

T20

R49•

S52

I53

R72

A78

G90•

T91•

W107

S108

I109

N110

R111

D112

R113

L118

S178

E184

Q189

A245•

A246•

Q247•

L292

L295

R296

L297

P315

M316

V317

P318

S375

LYS

VAL

ALA

S379•

P380•

T381

Y382•

L383•

E387•

A431

V432

A433•

N434•

H435

S436•

D437•

L438

T439

S440•

I441•

E449

R452

L457•

SER

HIS

LEU

SER

• Molecule 1: Kynurenine 3-monooxygenase

Chain B:

MET

THR

ALA

THR

ASP

ASN

A7

T20

R49•

G50•

A56

R72

R84

M85

V86

H87

V88

T91•

Y98

G99

R100•

I106

R111

D112

R113

L114

N115

L118

E184

H185

Q189

L213

H214

I215

I224

P244•

A245•

A246•

Q247•

P248•

A249•

S250•

A254•

V257•

R264•

F265•

R268•

F284•

L292

L297

V317

P318

E372

K376

V377•

A378•

S379•

Y382•

L383•

L384

F409

L427

D437

L438•

T439•

E449

L457

SER

HIS

LEU

SER

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


4 Data and re�nement statistics iO

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

69.48Å 53.31Å 135.84Å90.00◦ 104.50◦ 90.00◦

Depositor

Resolution (Å)43.84 � 1.8243.84 � 1.82

DepositorEDS

% Data completeness(in resolution range)

97.5 (43.84-1.82)97.5 (43.84-1.82)

DepositorEDS

Rmerge 0.06 DepositorRsym (Not available) Depositor

< I/σ(I) > 1 1.60 (at 1.82Å) XtriageRe�nement program BUSTER 2.11.6 Depositor

R, Rfree0.175 , 0.2100.180 , 0.214

DepositorDCC

Rfree test set 4295 re�ections (5.08%) wwPDB-VPWilson B-factor (Å2) 28.2 Xtriage

Anisotropy 0.066 XtriageBulk solvent ksol(e/Å3), Bsol(Å2) 0.34 , 51.2 EDS

L-test for twinning2 < |L| > = 0.49, < L2 > = 0.32 XtriageEstimated twinning fraction 0.000 for h,-k,-h-l Xtriage

Fo,Fc correlation 0.97 EDSTotal number of atoms 7917 wwPDB-VP

Average B, all atoms (Å2) 38.0 wwPDB-VP

Xtriage's analysis on translational NCS is as follows: The analyses of the Patterson function reveals

a signi�cant o�-origin peak that is 36.89 % of the origin peak, indicating pseudo-translational

symmetry. The chance of �nding a peak of this or larger height randomly in a structure without

pseudo-translational symmetry is equal to 4.6642e-04. The detected translational NCS is most

likely also responsible for the elevated intensity ratio.

1Intensities estimated from amplitudes.2Theoretical values of < |L| >, < L2 > for acentric re�ections 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 iO

5.1 Standard geometry iO

Bond lengths and bond angles in the following residue types are not validated in this section: GOL,8EQ, FAD, 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 ChainBond lengths Bond anglesRMSZ #|Z| >5 RMSZ #|Z| >5

1 A 0.53 0/3566 0.61 0/48441 B 0.50 0/3579 0.59 0/4862All All 0.52 0/7145 0.60 0/9706

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 iO

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 3482 0 3443 11 01 B 3497 0 3463 15 02 A 53 0 31 1 02 B 53 0 31 0 03 A 1 0 0 1 03 B 1 0 0 1 04 A 57 0 0 2 04 B 38 0 0 1 05 A 6 0 8 0 05 B 6 0 8 0 06 A 393 0 0 2 0

Continued on next page...

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


Continued from previous page...

Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes6 B 330 0 0 0 0All All 7917 0 6984 26 0

The all-atom clashscore is de�ned as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 2.

All (26) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2Interatomicdistance (Å)

Clashoverlap (Å)

1:B:84:ARG:HD2 1:B:215:ILE:HD12 1.53 0.881:A:184:GLU:HG2 1:A:297:LEU:HD22 1.58 0.841:B:184:GLU:HG2 1:B:297:LEU:HD22 1.66 0.771:B:318:PRO:HA 3:B:502:CL:CL 2.36 0.621:A:318:PRO:HA 3:A:502:CL:CL 2.38 0.611:A:189:GLN:HG3 1:A:317:VAL:HG11 1.84 0.591:B:384:LEU:HD11 1:B:437:ASP:HA 1.84 0.581:B:189:GLN:HG3 1:B:317:VAL:HG11 1.92 0.521:B:86:VAL:HG12 1:B:88:VAL:HG23 1.93 0.511:B:213:LEU:HD21 1:B:224:ILE:HD11 1.95 0.492:A:501:FAD:H6 4:A:503:8EQ:C 2.44 0.481:A:449:GLU:OE1 1:B:185:HIS:NE2 2.46 0.471:B:292:LEU:HD22 1:B:318:PRO:HD3 1.98 0.461:B:427:LEU:HD22 1:B:449:GLU:HB3 1.98 0.451:B:372:GLU:HA 1:B:376:LYS:HB2 1.98 0.451:B:20:THR:OG1 1:B:118:LEU:HB3 2.18 0.431:A:109:ILE:HD12 6:A:662:HOH:O 2.18 0.431:B:56:ALA:HB1 1:B:106:ILE:HG21 2.00 0.431:A:295:LEU:HB3 1:A:315:PRO:HD2 2.00 0.431:B:84:ARG:HD3 4:B:503:8EQ:O4 2.18 0.431:A:431:ALA:HB2 4:A:505:8EQ:CL 2.56 0.431:A:78:ALA:HB1 1:A:107:TRP:HB3 2.01 0.421:B:98:TYR:HB3 1:B:409:PHE:CZ 2.54 0.421:A:292:LEU:HD22 1:A:318:PRO:HD3 2.02 0.421:A:178:SER:HB3 6:A:695:HOH:O 2.21 0.41

1:A:20[A]:THR:OG1 1:A:118:LEU:HB3 2.21 0.41

There are no symmetry-related clashes.


5.3 Torsion angles iO

5.3.1 Protein backbone iO

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 447/461 (97%) 440 (98%) 7 (2%) 0 100 100

1 B 451/461 (98%) 444 (98%) 7 (2%) 0 100 100

All All 898/922 (97%) 884 (98%) 14 (2%) 0 100 100

There are no Ramachandran outliers to report.

5.3.2 Protein sidechains iO

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 364/372 (98%) 355 (98%) 9 (2%) 47 33

1 B 365/372 (98%) 360 (99%) 5 (1%) 67 58

All All 729/744 (98%) 715 (98%) 14 (2%) 57 45

All (14) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 A 52 SER1 A 53 ILE1 A 72 ARG1 A 111 ARG1 A 113 ARG1 A 438 LEU1 A 439 THR1 A 449 GLU


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



Mol Chain Res Type1 A 452 ARG1 B 72 ARG1 B 111 ARG1 B 113 ARG1 B 115 ASN1 B 438 LEU

Some sidechains can be �ipped to improve hydrogen bonding and reduce clashes. There are nosuch sidechains identi�ed.

5.3.3 RNA iO

There are no RNA molecules in this entry.

5.4 Non-standard residues in protein, DNA, RNA chains iO

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

5.5 Carbohydrates iO

There are no carbohydrates in this entry.

5.6 Ligand geometry iO

Of 11 ligands modelled in this entry, 2 are monoatomic - leaving 9 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 de�ned 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 LinkBond lengths Bond angles

Counts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2

4 8EQ B 504 - 11,20,20 0.88 0 12,28,28 0.80 05 GOL A 506 - 5,5,5 0.14 0 5,5,5 0.22 04 8EQ A 505 - 11,20,20 0.84 0 12,28,28 0.88 04 8EQ A 503 - 11,20,20 0.90 0 12,28,28 0.72 0

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

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




Mol Type Chain Res LinkBond lengths Bond angles

Counts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2

2 FAD A 501 - 51,58,58 1.38 4 (7%) 60,89,89 2.15 6 (10%)

2 FAD B 501 - 51,58,58 1.46 5 (9%) 60,89,89 2.13 6 (10%)5 GOL B 505 - 5,5,5 0.06 0 5,5,5 0.15 04 8EQ B 503 - 11,20,20 0.83 0 12,28,28 0.76 04 8EQ A 504 - 11,20,20 0.91 0 12,28,28 0.76 0

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

Mol Type Chain Res Link Chirals Torsions Rings4 8EQ B 504 - - 1/6/8/8 0/2/2/25 GOL A 506 - - 0/4/4/4 -4 8EQ A 505 - - 1/6/8/8 0/2/2/24 8EQ A 503 - - 0/6/8/8 0/2/2/22 FAD A 501 - - 2/30/50/50 0/6/6/62 FAD B 501 - - 1/30/50/50 0/6/6/65 GOL B 505 - - 0/4/4/4 -4 8EQ B 503 - - 1/6/8/8 0/2/2/24 8EQ A 504 - - 1/6/8/8 0/2/2/2

All (9) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)2 A 501 FAD C4X-C10 7.16 1.46 1.382 B 501 FAD C4X-C10 7.06 1.45 1.382 B 501 FAD C9A-N10 3.85 1.43 1.382 A 501 FAD C4-N3 3.67 1.39 1.332 B 501 FAD C4-N3 3.47 1.39 1.332 B 501 FAD C4-C4X 2.82 1.46 1.412 A 501 FAD C9A-N10 2.72 1.42 1.382 B 501 FAD C5X-N5 2.61 1.39 1.352 A 501 FAD C4-C4X 2.21 1.45 1.41

All (12) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)2 A 501 FAD C4-N3-C2 12.58 125.76 115.142 B 501 FAD C4-N3-C2 12.42 125.63 115.142 A 501 FAD C4X-C4-N3 -6.59 114.42 123.43




Mol Chain Res Type Atoms Z Observed(o) Ideal(o)2 B 501 FAD C4X-C4-N3 -6.50 114.55 123.432 A 501 FAD C10-C4X-N5 4.54 124.40 121.262 B 501 FAD C10-C4X-N5 4.38 124.29 121.262 A 501 FAD C4-C4X-C10 -3.72 117.49 119.952 A 501 FAD C4X-C10-N10 -3.67 116.53 120.302 B 501 FAD C4X-C10-N10 -3.62 116.58 120.302 B 501 FAD C4-C4X-C10 -3.52 117.62 119.952 A 501 FAD C5A-C6A-N6A 2.18 123.67 120.352 B 501 FAD C5A-C6A-N6A 2.13 123.59 120.35

There are no chirality outliers.

All (7) torsion outliers are listed below:

Mol Chain Res Type Atoms4 B 504 8EQ C7-C6-N-C94 A 505 8EQ N-C6-C7-C84 A 504 8EQ C7-C6-N-C94 B 503 8EQ C11-C2-O-C12 A 501 FAD O4B-C4B-C5B-O5B2 B 501 FAD O4B-C4B-C5B-O5B2 A 501 FAD C1'-C2'-C3'-O3'

There are no ring outliers.

4 monomers are involved in 3 short contacts:

Mol Chain Res Type Clashes Symm-Clashes4 A 505 8EQ 1 04 A 503 8EQ 1 02 A 501 FAD 1 04 B 503 8EQ 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 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 identi�ed 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 identi�ed 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-identi�ed 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 �nd su�cient


equivalents in the CSD to analyse the geometry.

Ligand 8EQ B 504

Bond lengths Bond angles

Torsions Rings

Ligand 8EQ A 505


Torsions Rings


Ligand FAD A 501


Torsions Rings


Ligand FAD B 501


Torsions Rings

Ligand 8EQ B 503


Torsions Rings


Ligand 8EQ A 504


Torsions Rings

5.7 Other polymers iO

There are no such residues in this entry.

5.8 Polymer linkage issues iO

There are no chain breaks in this entry.


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


6 Fit of model and data iO

6.1 Protein, DNA and RNA chains iO

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 448/461 (97%) -0.12 18 (4%) 38 32 19, 29, 69, 100 0

1 B 451/461 (97%) -0.07 24 (5%) 26 21 20, 34, 70, 104 0

All All 899/922 (97%) -0.09 42 (4%) 31 25 19, 32, 70, 104 0

All (42) RSRZ outliers are listed below:

Mol Chain Res Type RSRZ1 A 383 LEU 9.21 B 246 ALA 7.71 B 245 ALA 7.71 A 436 SER 7.11 A 90 GLY 6.71 B 257 VAL 6.61 B 247 GLN 6.21 A 379 SER 5.21 B 249 ALA 5.11 A 380 PRO 4.71 B 248 PRO 3.91 B 244 PRO 3.91 B 250 SER 3.81 A 457 LEU 3.51 B 382 TYR 3.31 B 49 ARG 3.31 A 433 ALA 3.31 A 434 ASN 3.31 A 440 SER 3.21 B 383 LEU 3.21 A 382 TYR 3.01 B 378 ALA 2.91 A 91 THR 2.81 B 379 SER 2.8


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

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



Mol Chain Res Type RSRZ1 A 387 GLU 2.81 B 439 THR 2.81 B 265 PHE 2.81 A 245 ALA 2.71 A 246 ALA 2.71 B 254 ALA 2.61 A 247 GLN 2.61 A 437 ASP 2.41 B 50 GLY 2.41 B 284 PHE 2.41 B 100 ARG 2.31 A 441 ILE 2.21 B 438 LEU 2.21 A 49 ARG 2.11 B 377 VAL 2.11 B 268 ARG 2.11 B 264 ARG 2.01 B 91 THR 2.0

6.2 Non-standard residues in protein, DNA, RNA chains iO

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

6.3 Carbohydrates iO

There are no carbohydrates in this entry.

6.4 Ligands iO

In the following table, the Atoms column lists the number of modelled atoms in the group and thenumber de�ned 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<0.94 8EQ A 505 19/19 0.84 0.19 46,56,73,74 04 8EQ A 504 19/19 0.85 0.17 24,55,72,75 04 8EQ B 504 19/19 0.86 0.20 26,54,80,80 05 GOL A 506 6/6 0.93 0.11 32,40,43,45 05 GOL B 505 6/6 0.96 0.10 35,40,45,49 0


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





Mol Type Chain Res Atoms RSCC RSR B-factors(Å2) Q<0.94 8EQ A 503 19/19 0.96 0.07 23,27,37,39 04 8EQ B 503 19/19 0.97 0.08 25,30,41,41 02 FAD B 501 53/53 0.98 0.08 20,24,33,34 02 FAD A 501 53/53 0.98 0.09 17,21,27,29 03 CL B 502 1/1 0.99 0.08 31,31,31,31 03 CL A 502 1/1 1.00 0.09 27,27,27,27 0

The following is a graphical depiction of the model �t to experimental electron density of allinstances of the Ligand of Interest. In addition, ligands with molecular weight > 250 and outliersas shown on the geometry validation Tables will also be included. Each �t is shown from di�erentorientation to approximate a three-dimensional view.

Electron density around 8EQ A 505:

2mFo-DFc (at 0.7 rmsd) in gray

mFo-DFc (at 3 rmsd) in purple (negative)

and green (positive)


Electron density around 8EQ A 504:




Electron density around 8EQ B 504:





Electron density around 8EQ B 503:




Electron density around FAD B 501:





Electron density around FAD A 501:




6.5 Other polymers iO

There are no such residues in this entry.


Documents

Full wwPDB X-ray Structure Validation Report O i · 2020. 5. 31. · Stretches of 2 or more consecutive residues without any outlier are shown as a green connector. Residues present