iFull wwPDB X-ray Structure Validation Report ○Oct 5, 2023 – 07:53 AM EDTPDB ID : 6W02
Title : Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 inthe complex with ADP riboseAuthors : Michalska, K.; Kim, Y.; Jedrzejczak, R.; Maltseva, N.; Endres, M.; Mesecar,A.; Joachimiak, A.; Center for Structural Genomics of Infectious Diseases(CSGID)
Deposited on : 2020-02-28
Resolution : 1.50 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.org
A user guide is available athttps://www.wwpdb.org/validation/2017/XrayValidationReportHelp
i symbol.
with specific help available everywhere you see the ○The types of validation reports are described at
http://www.wwpdb.org/validation/2017/FAQs#types.

i were used in the production of this report:
The following versions of software and data (see references ○)MolProbity
Mogul
Xtriage (Phenix)
EDS
buster-report
Percentile statistics
Ideal geometry (proteins)
Ideal geometry (DNA, RNA)
Validation Pipeline (wwPDB-VP):::::::::

FAILED
1.8.5 (274361), CSD as541be (2020)
1.13
FAILED
1.1.7 (2018)20191225.v01 (using entries in the PDB archive December 25th 2019)Engh & Huber (2001)
Parkinson et al. (1996)
2.35.1

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6W02

iOverall quality at a glance ○The following experimental techniques were used to determine the structure:
X-RAY DIFFRACTION
The reported resolution of this entry is 1.50 Å.
There are no overall percentile quality scores available for this entry.
MolProbity and EDS failed to run properly - the sequence quality summary graphics cannot beshown.

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6W02

iEntry composition ○There are 4 unique types of molecules in this entry. The entry contains 3016 atoms, of which 0are hydrogens and 0 are deuteriums.
In the tables below, the ZeroOcc column contains the number of atoms modelled with zero occupancy, the AltConf column contains the number of residues with at least one atom in alternate
conformation and the Trace column contains the number of residues modelled with at most 2atoms.
• Molecule 1 is a protein called Non-structural protein 3.
Mol

ChainResidues

1A165

1B

167

Atoms
Total CNO S
1276 808 223 241 4Total C
NO S
1291 819 224 244 4

ZeroOcc

AltConf

Trace

030030

There are 2 discrepancies between the modelled and reference sequences:
ChainA
B

Residue
11Modelled
GLY
GLY

Actual-Comment
expression tag
expression tag

Reference
UNP P0DTD1
UNP P0DTD1• Molecule 2 is ADENOSINE-5-DIPHOSPHORIBOSE (three-letter code: APR) (formula:C15 H23 N5 O14 P2 ) (labeled as "Ligand of Interest" by depositor).

Mol

ChainResidues

2A

1Total36Atoms
C N O
15 5 14

ZeroOcc AltConf
P002
Continued on next page...

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Continued from previous page...
Mol Chain Residues
Atoms
Total C N O
2B1
36
15 5 14

P26W02

ZeroOcc

AltConf00• Molecule 3 is 1,2-ETHANEDIOL (three-letter code: EDO) (formula: C2 H6 O2 ).

MolChainResidues

3A

1AtomsTotal C O
42 2

ZeroOcc

AltConf00• Molecule 4 is water.
MolChain

Residues

4A

179

4B

194

Atoms
Total O179 179
Total O
194 194

ZeroOcc

AltConf0000

MolProbity and EDS failed to run properly - this section is therefore empty.

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iData and refinement statistics ○EDS failed to run properly - this section is therefore incomplete.
Property
Space group
Cell constantsa, b, c, α, β, γResolution (Å)% Data completeness(in resolution range)
RmergeRsym< I/σ(I) > 1
Refinement program
R, Rf reeWilson B-factor (Å2 )Anisotropy
L-test for twinning2
Estimated twinning fraction
Total number of atoms
Average B, all atoms (Å2 )Value
P133.26Å 37.84Å 68.30Å
97.86◦ 97.38◦ 89.94◦
37.48 – 1.50

SourceDepositor

79.8 (37.48-1.50)

Depositor

0.07(Not available)
1.86 (at 1.32Å)PHENIX 1.13_2998
0.150 , 0.173
16.1
0.726
< |L| > = 0.50, < L2 > = 0.33
No twinning to report.
3016
22.0

Depositor
Depositor
Xtriage
Depositor
Depositor
Xtriage
Xtriage
Xtriage
Xtriage
wwPDB-VP
wwPDB-VPDepositor
Depositor

Xtriage’s analysis on translational NCS is as follows: The largest off-origin peak in the Patterson
function is 9.63% of the height of the origin peak. No significant pseudotranslation is detected.

Intensities estimated from amplitudes.
Theoretical 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.
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iModel quality ○iStandard geometry ○MolProbity failed to run properly - this section is therefore empty.

4.2

i
Too-close contacts ○MolProbity failed to run properly - this section is therefore empty.

4.3

i
Torsion angles ○

4.3.1

i
Protein backbone ○MolProbity failed to run properly - this section is therefore empty.
4.3.2

iProtein sidechains ○MolProbity failed to run properly - this section is therefore empty.
4.3.3

i
RNA ○

MolProbity failed to run properly - this section is therefore empty.

4.4i
Non-standard residues in protein, DNA, RNA chains ○There are no non-standard protein/DNA/RNA residues in this entry.

4.5i
Carbohydrates ○There are no monosaccharides in this entry.

4.6

i
Ligand geometry ○3 ligands are modelled in this entry.
In the following table, the Counts columns list the number of bonds (or angles) for which Mogul
statistics 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 bond

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6W02length (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).

-Bond lengths
Counts RMSZ #|Z| > 2
3,3,30.44
034,39,390.58
0Bond angles
Counts RMSZ #|Z| > 2
2,2,20.29
040,60,600.73
1 (2%)-34,39,39

40,60,60

Mol

Type

ChainRes

Link

32

EDO
APRA
A

202
201

2APR

B

201

0.56

00.70

1 (2%)In the following table, the Chirals column lists the number of chiral outliers, the number of chiral
centers 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
322

Type
EDO
APR
APR

ChainAA
B

Res
202
201
201

Link-Chirals-Torsions
0/1/1/1
1/18/54/54
0/18/54/54

Rings
0/4/4/4
0/4/4/4

There are no bond length outliers.
All (2) bond angle outliers are listed below:
Mol
22Chain
AB

Res
201
201

TypeAPRAPR

Atoms
C5-C6-N6
C5-C6-N6Z
2.44
2.18

Observed(o )124.07
123.66

Ideal(o )120.35120.35

There are no chirality outliers.
All (1) torsion outliers are listed below:
Mol2Chain
ARes
201

Type
APR

Atoms
C5’-O5’-PA-O1A

There are no ring outliers.
No monomer is involved in short contacts.
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 will
also 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 identified as an outlier by Mogul will behighlighted in the graph. For rings, the root-mean-square deviation (RMSD) between the ring

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6W02in question and similar rings identified 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-identified 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 find sufficientequivalents in the CSD to analyse the geometry.
Ligand APR A 201

Bond lengths

Bond angles

Torsions

Rings

Ligand APR B 201

4.7

Bond lengths

Bond angles

Torsions

Rings

i
Other polymers ○There are no such residues in this entry.

4.8i
Polymer linkage issues ○There are no chain breaks in this entry.

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Fit of model and data ○iProtein, DNA and RNA chains ○EDS failed to run properly - this section is therefore empty.

5.2i
Non-standard residues in protein, DNA, RNA chains ○EDS failed to run properly - this section is therefore empty.

5.3i
Carbohydrates ○EDS failed to run properly - this section is therefore empty.

5.4i
Ligands ○EDS failed to run properly - this section is therefore empty.

5.5iOther polymers ○EDS failed to run properly - this section is therefore empty.

6W02