full wwpdb x-ray structure validation report o i1226 768 210 242 6 0 0 0 there are 6 discrepancies...

Full wwPDB X-ray Structure Validation Report iO

May 18, 2020 � 10:08 am BST

PDB ID : 6NTCTitle : Crystal Structure of G12V HRas-GppNHp bound in complex with the engi-

neered RBD variant 1 of CRAF Kinase proteinAuthors : Maisonneuve, P.; Kurinov, I.; Wiechmann, S.; Ernst, A.; Sicheri, F.

Deposited on : 2019-01-28Resolution : 2.90 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] user guide is available at

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

Full wwPDB X-ray Structure Validation Report 6NTC

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 2.90 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 1957 (2.90-2.90)Clashscore 141614 2172 (2.90-2.90)

Ramachandran outliers 138981 2115 (2.90-2.90)Sidechain outliers 138945 2117 (2.90-2.90)RSRZ outliers 127900 1906 (2.90-2.90)

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


2 Entry composition iO

There are 6 unique types of molecules in this entry. The entry contains 1658 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 GTPase HRas.

Mol Chain Residues Atoms ZeroOcc AltConf Trace

1 A 168Total C N O S1226 768 210 242 6

0 0 0

There are 6 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceA -4 GLY - expression tag UNP P01112A -3 ALA - expression tag UNP P01112A -2 MET - expression tag UNP P01112A -1 ASP - expression tag UNP P01112A 0 PRO - expression tag UNP P01112A 12 VAL GLY engineered mutation UNP P01112

Molecule 2 is a protein called RAF proto-oncogene serine/threonine-protein kinase.

Mol Chain Residues Atoms ZeroOcc AltConf Trace

2 B 63Total C N O388 236 74 78

0 0 0

There are 14 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceB 51 GLY - expression tag UNP P04049B 52 ALA - expression tag UNP P04049B 53 MET - expression tag UNP P04049B 54 ASP - expression tag UNP P04049B 61 LEU PHE engineered mutation UNP P04049B 65 GLN LYS engineered mutation UNP P04049B 66 GLU GLN engineered mutation UNP P04049B 67 TRP ARG engineered mutation UNP P04049B 71 LYS ASN engineered mutation UNP P04049B 81 SER CYS engineered mutation UNP P04049

Continued on next page...

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


Continued from previous page...

Chain Residue Modelled Actual Comment ReferenceB 88 ARG VAL engineered mutation UNP P04049B 89 HIS ARG engineered mutation UNP P04049B 95 SER CYS engineered mutation UNP P04049B 96 SER CYS engineered mutation UNP P04049

Molecule 3 is PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (three-lettercode: GNP) (formula: C10H17N6O13P3).

Mol Chain Residues Atoms ZeroOcc AltConf

3 A 1Total C N O P32 10 6 13 3

0 0

Molecule 4 is GLYCEROL (three-letter code: GOL) (formula: C3H8O3).



4 A 1Total C O6 3 3

0 0

Molecule 5 is MAGNESIUM ION (three-letter code: MG) (formula: Mg).


5 A 1Total Mg1 1

0 0

Molecule 6 is water.


6 A 5Total O5 5

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: GTPase HRas

Chain A:

GLY

ALA

MET

D-1

V9

G10

A11

V12

K16

I24

Q25

D38

I46•

D47

L56•

G77•

F78

V81•

H94

Q95

Y96

R97

E98

Q99

I100

M111

V114•

A122•

I142

E153•

D154

A155•

L159

I163

R164

Q165

H166

• Molecule 2: RAF proto-oncogene serine/threonine-protein kinase

Chain B:

GLY

ALA

MET

ASP

SER

N56

L61

E66

W67

V72

ARG

ASN

GLY

M76

R88

H89

V98

F99

ARG

LEU

LEU

HIS

GLU

HIS

LYS

GLY

LYS

K109

A110

R111

A118

A119

I122

V128•

D129

F130

LEU

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


4 Data and re�nement statistics iO

Property Value SourceSpace group P 63 2 2 DepositorCell constantsa, b, c, α, β, γ

91.62Å 91.62Å 151.41Å90.00◦ 90.00◦ 120.00◦

Depositor

Resolution (Å)79.34 � 2.9079.34 � 2.90

DepositorEDS

% Data completeness(in resolution range)

95.6 (79.34-2.90)95.6 (79.34-2.90)

DepositorEDS

Rmerge 0.14 DepositorRsym (Not available) Depositor

< I/σ(I) > 1 0.96 (at 2.91Å) XtriageRe�nement program PHENIX 1.16_3549 Depositor

R, Rfree0.252 , 0.2780.252 , 0.279

DepositorDCC

Rfree test set 449 re�ections (5.29%) wwPDB-VPWilson B-factor (Å2) 115.0 Xtriage

Anisotropy 0.376 XtriageBulk solvent ksol(e/Å3), Bsol(Å2) 0.32 , 140.8 EDS

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

Fo,Fc correlation 0.93 EDSTotal number of atoms 1658 wwPDB-VP

Average B, all atoms (Å2) 145.0 wwPDB-VP

Xtriage's analysis on translational NCS is as follows: The largest o�-origin peak in the Pattersonfunction is 7.73% of the height of the origin peak. No signi�cant pseudotranslation is detected.

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,GNP, MG

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 0.24 0/1244 0.42 0/16962 B 0.22 0/391 0.40 0/537All All 0.23 0/1635 0.41 0/2233

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 1226 0 1122 11 02 B 388 0 279 7 03 A 32 0 13 3 04 A 6 0 8 0 05 A 1 0 0 0 06 A 5 0 0 0 0All All 1658 0 1422 18 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 6.

All (18) close contacts within the same asymmetric unit are listed below, sorted by their clash

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


magnitude.

Atom-1 Atom-2Interatomicdistance (Å)

Clashoverlap (Å)

1:A:24:ILE:HG22 1:A:25:GLN:HG3 1.74 0.691:A:78:PHE:HB2 1:A:111:MET:HG2 1.83 0.601:A:77:GLY:HA3 1:A:163:ILE:HD11 1.85 0.581:A:47:ASP:OD2 1:A:164:ARG:NH2 2.28 0.561:A:38:ASP:OD2 2:B:88:ARG:NH1 2.38 0.561:A:12:VAL:O 3:A:201:GNP:N3B 2.44 0.512:B:98:VAL:HA 2:B:128:VAL:HG22 1.93 0.491:A:11:ALA:O 1:A:16:LYS:NZ 2.46 0.482:B:99:PHE:HA 2:B:111:ARG:HA 1.95 0.482:B:61:LEU:HA 2:B:67:TRP:HB3 1.96 0.462:B:66:GLU:HB3 2:B:89:HIS:CE1 2.50 0.461:A:96:TYR:O 1:A:100:ILE:HG12 2.16 0.462:B:76:MET:O 2:B:118:ALA:N 2.42 0.461:A:94:HIS:O 1:A:98:GLU:HG2 2.16 0.45

2:B:72:VAL:HG21 2:B:119:ALA:HB2 2.00 0.443:A:201:GNP:H5'2 3:A:201:GNP:H8 2.02 0.411:A:159:LEU:O 1:A:163:ILE:HG13 2.21 0.411:A:16:LYS:NZ 3:A:201:GNP:O2G 2.50 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 166/171 (97%) 156 (94%) 10 (6%) 0 100 100

2 B 57/81 (70%) 53 (93%) 4 (7%) 0 100 100

All All 223/252 (88%) 209 (94%) 14 (6%) 0 100 100

There are no Ramachandran outliers to report.

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


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 119/148 (80%) 117 (98%) 2 (2%) 60 86

2 B 25/70 (36%) 24 (96%) 1 (4%) 31 65

All All 144/218 (66%) 141 (98%) 3 (2%) 53 81

All (3) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 A 9 VAL1 A 142 ILE2 B 122 ILE

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 3 ligands modelled in this entry, 1 is monoatomic - leaving 2 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 and

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


the 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| > 24 GOL A 202 - 5,5,5 0.91 0 5,5,5 1.04 03 GNP A 201 5 28,34,34 2.36 10 (35%) 30,54,54 1.86 4 (13%)

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 GOL A 202 - - 2/4/4/4 -

3 GNP A 201 5 - 8/17/38/38 0/3/3/3

All (10) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)3 A 201 GNP C4-N9 -7.33 1.38 1.473 A 201 GNP C5-C6 -4.55 1.45 1.523 A 201 GNP PB-O3A 4.52 1.64 1.593 A 201 GNP PB-O1B 3.19 1.51 1.463 A 201 GNP C6-N1 3.10 1.38 1.333 A 201 GNP PG-N3B 3.03 1.71 1.633 A 201 GNP PG-O1G 2.71 1.50 1.463 A 201 GNP C5-C4 -2.38 1.38 1.533 A 201 GNP C8-N9 -2.37 1.37 1.453 A 201 GNP PB-O2B -2.18 1.50 1.56

All (4) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)3 A 201 GNP C4-C5-N7 6.11 110.56 102.463 A 201 GNP C5-C6-N1 -5.11 111.89 118.193 A 201 GNP O6-C6-C5 3.71 127.44 119.863 A 201 GNP PA-O3A-PB -2.79 122.78 132.62

There are no chirality outliers.


All (10) torsion outliers are listed below:

Mol Chain Res Type Atoms3 A 201 GNP PB-N3B-PG-O1G3 A 201 GNP PG-N3B-PB-O1B3 A 201 GNP C5'-O5'-PA-O3A3 A 201 GNP C2'-C1'-N9-C43 A 201 GNP O4'-C4'-C5'-O5'4 A 202 GOL C1-C2-C3-O33 A 201 GNP C3'-C4'-C5'-O5'3 A 201 GNP C5'-O5'-PA-O1A3 A 201 GNP C5'-O5'-PA-O2A4 A 202 GOL O2-C2-C3-O3

There are no ring outliers.

1 monomer is involved in 3 short contacts:

Mol Chain Res Type Clashes Symm-Clashes3 A 201 GNP 3 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�cientequivalents in the CSD to analyse the geometry.


Ligand GNP A 201

Bond lengths Bond angles

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#nonstandard_residues_and_ligandshttps://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>2 OWAB(Å2) Q


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 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 GNP A 201:

2mFo-DFc (at 0.7 rmsd) in gray

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

and green (positive)

6.5 Other polymers iO

There are no such residues in this entry.

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

Overall quality at a glanceEntry compositionResidue-property plotsData and refinement statisticsModel qualityStandard geometryToo-close contactsTorsion anglesProtein backboneProtein sidechainsRNA

Non-standard residues in protein, DNA, RNA chainsCarbohydratesLigand geometryOther polymersPolymer linkage issues

Fit of model and data i Protein, DNA and RNA chains i Non-standard residues in protein, DNA, RNA chains i Carbohydrates i Ligands i Other polymers i

full wwpdb x-ray structure validation report o i1226 768 210 242 6 0 0 0 there are 6 discrepancies...

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