iFull wwPDB X-ray Structure Validation Report ○Oct 5, 2023 – 06:31 AM EDTPDB ID : 6VYOTitle : Crystal structure of RNA binding domain of nucleocapsid phosphoprotein fromSARS coronavirus 2Authors : Chang, C.; Michalska, K.; Jedrzejczak, R.; Maltseva, N.; Endres, M.; Godzik,A.; Kim, Y.; Joachimiak, A.; Center for Structural Genomics of Infectious
Diseases (CSGID)
Deposited on : 2020-02-27
Resolution : 1.70 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
Percentile statistics
Ideal geometry (proteins)
Ideal geometry (DNA, RNA)
Validation Pipeline (wwPDB-VP)::::::::

FAILED
1.8.5 (274361), CSD as541be (2020)
1.13
FAILED20191225.v01 (using entries in the PDB archive December 25th 2019)Engh & Huber (2001)
Parkinson et al. (1996)
2.35.1

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6VYOi
Overall quality at a glance ○The following experimental techniques were used to determine the structure:
X-RAY DIFFRACTION
The reported resolution of this entry is 1.70 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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6VYOiEntry composition ○There are 6 unique types of molecules in this entry. The entry contains 4683 atoms, of which 0
are 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 Nucleoprotein.
MolChainResidues

1A

124

1B

125

1C125

1D125

Total
974
Total
981
Total
1002
Total
982

Atoms
CN
618 175CN621 177CN
633 180CN
622 176

O
180
O
182
O
188
O
183

S
1S
1S
1S
1ZeroOcc

AltConf

Trace

0100

100

400

10

There are 4 discrepancies between the modelled and reference sequences:
ChainA
B
CD

Residue
46
46
46
46

Modelled
GLY
GLY
GLY
GLY

Actual-Comment
expression tag
expression tag
expression tag
expression tag

Reference
UNP P0DTC9UNP P0DTC9UNP P0DTC9UNP P0DTC9• Molecule 2 is 2-(N-MORPHOLINO)-ETHANESULFONIC ACID (three-letter code: MES)
(formula: C6 H13 NO4 S).

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MolChainResidues

2A

12A

12B

12C

1Total12Total
12Total
12Total
12Atoms
C N O
6 1 4
C N O
6 1 4
C N O
6 1 4
C N O
6 1 4S
1S
1S
1S
1ZeroOcc

AltConf00000000• Molecule 3 is CHLORIDE ION (three-letter code: CL) (formula: Cl).
MolChainResidues

3A

23C2Atoms
Total Cl
22Total Cl
22ZeroOcc

AltConf0000• Molecule 4 is ZINC ION (three-letter code: ZN) (formula: Zn).
Mol

Chain

Residues

4A

24B

14C

1AtomsTotal Zn
22Total Zn
11Total Zn
11

ZeroOcc

AltConf0000006VYO

Page 5Full wwPDB X-ray Structure Validation Report• Molecule 5 is GLYCEROL (three-letter code: GOL) (formula: C3 H8 O3 ).

Mol

Chain

Residues

5B

15C

15D

15D1Atoms
Total C O
63 3
Total C O
63 3
Total C O
63 3
Total C O
63 3

ZeroOcc

AltConf00000000• Molecule 6 is water.
MolChainResidues

6A

168

6B

157

6C

162

6D177

Atoms
Total O168 168
Total O
157 157
Total O
162 162
Total O
177 177

ZeroOcc

AltConf00000000

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

6VYOPage 63Full wwPDB X-ray Structure Validation Report

6VYOi
Data 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
P 21 21 2166.24Å 77.43Å 114.04Å
90.00◦ 90.00◦
90.00◦
46.05 – 1.70

SourceDepositor

87.3 (46.05-1.70)

Depositor

0.13(Not available)
3.93 (at 1.70Å)
PHENIX 1.17.1_3660
0.159 , 0.205
13.70.248< |L| > = 0.51, < L2 > = 0.34
No twinning to report.
4683
22.0

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

Depositor
Depositor

Xtriage’s analysis on translational NCS is as follows: The analyses of the Patterson function reveals
a significant off-origin peak that is 41.67 % of the origin peak, indicating pseudo-translational
symmetry. The chance of finding a peak of this or larger height randomly in a structure without
pseudo-translational symmetry is equal to 2.2808e-04. The detected translational NCS is most
likely also responsible for the elevated intensity ratio.

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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6VYOi
Model 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 ○Of 16 ligands modelled in this entry, 8 are monoatomic - leaving 8 for Mogul analysis.
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. The
Link column lists molecule types, if any, to which the group is linked. The Z score for a bond

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6VYOlength (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
12,12,122.28
1 (8%)

Bond angles
Counts RMSZ #|Z| > 2
14,16,16
2.23
7 (50%)-

12,12,12
5,5,55,5,55,5,5
12,12,12
5,5,512,12,12

14,16,16
5,5,5
5,5,5
5,5,5
14,16,16
5,5,5
14,16,16

Mol

Type

ChainRes

Link

2MES

A

201

2
5
5
52
52

MES
GOL
GOL
GOL
MES
GOL
MES

C
C
D
B
A
D
B

204
203
202
201
203
201
202

2.19
0.96
0.88
0.83
2.17
0.88
2.27

1 (8%)000
1 (8%)
01 (8%)

2.20
0.88
0.96
1.03
1.89
1.02
1.88

6 (42%)000
3 (21%)
03 (21%)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
2

TypeMES

ChainA

Res
201

Link-

Chirals-Torsions
3/6/14/14

Rings
0/1/1/1

2

MES

C

204

-

-

5/6/14/14

0/1/1/1

5
5
5

GOL
GOL
GOL

C
D
B

203
202
201

-

-

4/4/4/4
0/4/4/4
2/4/4/4

-

2

MES

A

203

-

-

4/6/14/14

0/1/1/1

5

GOL

D201

-

-

3/4/4/4-2MESB

202--

4/6/14/14

0/1/1/1

All (4) bond length outliers are listed below:
Mol22
22Chain
BACA

Res
202
201
204
203

Type
MES
MES
MES
MES

Atoms
C8-S
C8-S
C8-S
C8-S

Z
-7.62
-7.61
-7.33
-7.27

Observed(Å)
1.66
1.66
1.67
1.67

Ideal(Å)
1.77
1.77
1.77
1.77

All (19) bond angle outliers are listed below:
Mol
2Chain
ARes
201

TypeMES

Atoms
C5-N4-C3Z
4.98

Observed(o ) Ideal(o )120.03108.83
Continued on next page...

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Continued from previous page...
Mol Chain Res TypeAtoms
2B
202 MES C5-N4-C32A
203 MES C5-N4-C32C
204 MES C5-N4-C32C
204 MES C7-N4-C32A
203 MES O3S-S-C82C
204 MES O2S-S-C82A
201 MES C7-N4-C52A
201 MES C7-N4-C32C
204 MES O3S-S-C82A
201 MES O1S-S-C82C
204 MES C6-C5-N42A
201 MES O3S-S-C82C
204 MES C7-N4-C52B
202 MES O3S-S-C82A
201 MES C2-C3-N42A203 MES O2S-S-C82B
202 MES O2S-S-C82A
201 MES C6-C5-N4Z
4.67
4.47
4.39
3.21
3.03
3.01
2.82
2.58
2.53
2.50
-2.49
2.45
2.40
2.40
-2.35
2.30
2.10
-2.10

There are no chirality outliers.
All (25) torsion outliers are listed below:
Mol2222222255525252222Chain
A
A
A
A
B
B
C
C
B
C
C
C
B
B
C
A
A
B
C

Res TypeAtoms
201 MES C7-C8-S-O2S
201 MES C7-C8-S-O3S
203 MES C7-C8-S-O1S203 MES C7-C8-S-O3S
202 MES C7-C8-S-O1S
202 MES C7-C8-S-O3S
204 MES C8-C7-N4-C3
204 MES C7-C8-S-O2S
201 GOL O1-C1-C2-C3
203 GOL C1-C2-C3-O3
203 GOL O2-C2-C3-O3
204 MES C7-C8-S-O3S
201 GOL O1-C1-C2-O2
202 MES C8-C7-N4-C3
203 GOL O1-C1-C2-O2
201 MES C7-C8-S-O1S203 MES C7-C8-S-O2S
202 MES C7-C8-S-O2S
204 MES C7-C8-S-O1SContinued on next page...

Observed(o )119.35118.90118.71
119.43110.67110.54118.45117.82
109.86109.92106.33109.72117.37109.64106.54109.69109.44106.93

Ideal(o )108.83108.83108.83111.23105.77106.92111.23111.23105.77106.92110.10105.77111.23105.77110.10106.92106.92110.106VYOPage 10

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Continued from previous page...
Mol Chain Res Type
Atoms
5
D
201 GOL C1-C2-C3-O3
2
A
203 MES C8-C7-N4-C3
2C
204 MES C8-C7-N4-C5
5C
203 GOL O1-C1-C2-C3
5D
201 GOL O1-C1-C2-C3
5D
201 GOL O1-C1-C2-O2
There are no ring outliers.
No monomer is involved in short contacts.

4.7

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

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

6VYOPage 11

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5.1

Full wwPDB X-ray Structure Validation Reporti
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.

5.3

iCarbohydrates ○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.

6VYO