iFull wwPDB X-ray Structure Validation Report ○Mar 23, 2023 – 03:12 pm GMT
PDB ID : 6Y84
Title : SARS-CoV-2 main protease with unliganded active site (2019-nCoV, coronavirus disease 2019, COVID-19)
Authors : Owen, C.D.; Lukacik, P.; Strain-Damerell, C.M.; Douangamath, A.; Powell,A.J.; Fearon, D.; Brandao-Neto, J.; Crawshaw, A.D.; Aragao, D.; Williams,M.; Flaig, R.; Hall, D.R.; McAuley, K.E.; Mazzorana, M.; Stuart, D.I.; vonDelft, F.; Walsh, M.A.
Deposited on : 2020-03-03
Resolution : 1.39 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
MogulXtriage (Phenix)
EDS
Percentile statistics
Refmac
CCP4
Ideal geometry (proteins)
Ideal geometry (DNA, RNA):::::::::

4.02b-467
1.8.4, CSD as541be (2020)
1.13
2.32.1
20191225.v01 (using entries in the PDB archive December 25th 2019)
5.8.0158
7.0.044 (Gargrove)
Engh & Huber (2001)
Parkinson et al. (1996)

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6Y84

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 1.39 Å.
Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown in
the following graphic. The table shows the number of entries on which the scores are based.

MetricRf reeClashscore
Ramachandran outliers
Sidechain outliers
RSRZ outliers

Whole archive(#Entries)
130704141614138981138945127900Similar resolution(#Entries, resolution range(Å))
1714 (1.40-1.40)
1812 (1.40-1.40)
1763 (1.40-1.40)
1762 (1.40-1.40)
1674 (1.40-1.40)

The table below summarises the geometric issues observed across the polymeric chains and their
fit to the electron density. The red, orange, yellow and green segments of the lower bar indicate
the fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality
criteria 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 dot
representing fractions <=5% The upper red bar (where present) indicates the fraction of residues
that have poor fit to the electron density. The numeric value is given above the bar.
MolChain

Length1A306

Validation Pipeline (wwPDB-VP)

Quality of chain:

2.32.1

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6Y84i
Entry composition ○There are 3 unique types of molecules in this entry. The entry contains 2950 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 3C-like proteinase nsp5.
MolChainResidues

1A304

AtomsTotalCN2543 1604 433

O479

S27

ZeroOcc

AltConf

Trace0260• Molecule 2 is DIMETHYL SULFOXIDE (three-letter code: DMS) (formula: C2 H6 OS).

Mol

Chain

Residues

2A

12A

12

A

12A

1

• Molecule 3 is water.

Atoms
Total C O
42 1
Total C O
42 1
Total C O
42 1
Total C O
42 1

S1S1S1S1ZeroOcc

AltConf00000000

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MolChainResidues

3A391

AtomsTotal O391 391

ZeroOcc

AltConf

006Y84

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6Y84

iResidue-property plots ○These plots are drawn for all protein, RNA, DNA and oligosaccharide chains in the entry. The
first graphic for a chain summarises the proportions of the various outlier classes displayed in thesecond graphic. The second graphic shows the sequence view annotated by issues in geometry andelectron density. Residues are color-coded according to the number of geometric quality criteria
for which they contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more.
A red dot above a residue indicates a poor fit to the electron density (RSRZ > 2). Stretches of 2or more consecutive residues without any outlier are shown as a green connector. Residues present
in the sample, but not in the model, are shown in grey.
• Molecule 1: 3C-like proteinase nsp5•••
G302
V303T304
PHE
GLN

•
R298

F294

D197

V186
D187

•
G179

P168

•
M165

Y154

Y126
Q127
C128

S121
P122

T98

N95

V86
L87

N72
V73

L50

•
•
•
••
S46
E47

R40

L27

G23
T24

S1•••

Chain A:

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6Y84

iData and refinement statistics ○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 ree
Rf ree test set
Wilson B-factor (Å2 )Anisotropy
Bulk solvent ksol (e/Å3 ), Bsol (Å2 )L-test for twinning2
Estimated twinning fraction
Fo ,Fc correlation
Total number of atoms
Average B, all atoms (Å2 )

Value
C121
112.81Å 52.95Å 44.63Å
90.00◦ 103.16◦ 90.00◦
54.93 – 1.39
54.92 – 1.39
97.5 (54.93-1.39)
97.5 (54.92-1.39)
0.06(Not available)
1.34 (at 1.39Å)
BUSTER
0.178 , 0.200
0.186 , 0.172
2585 reflections (5.14%)
14.9
0.443
0.32 , 35.4
< |L| > = 0.50, < L2 > = 0.34
No twinning to report.
0.972950
20.0SourceDepositor
Depositor
Depositor
EDS
Depositor
EDS
Depositor
Depositor
Xtriage
Depositor
DepositorDCC
wwPDB-VP
Xtriage
Xtriage
EDS
Xtriage
XtriageEDS
wwPDB-VP
wwPDB-VP

Xtriage’s analysis on translational NCS is as follows: The largest off-origin peak in the Patterson
function is 9.95% 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 ○5.1iStandard geometry ○Bond lengths and bond angles in the following residue types are not validated in this section:DMS
The Z score for a bond length (or angle) is the number of standard deviations the observed value
is removed from the expected value. A bond length (or angle) with |Z| > 5 is considered an
outlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (orangles).
MolChain1A

Bond lengths
RMSZ #|Z| >50.37
0/2601

Bond angles
RMSZ #|Z| >50.59
0/3528There are no bond length outliers.
There are no bond angle outliers.
There are no chirality outliers.
There are no planarity outliers.

5.2

iToo-close contacts ○In the following table, the Non-H and H(model) columns list the number of non-hydrogen atoms
and 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 within
the asymmetric unit, whereas Symm-Clashes lists symmetry-related clashes.
Mol123AllChainAAAAll

Non-H2543
16391
2950

H(model)0000

H(added)2484
2402508

Clashes152115

Symm-Clashes
0000

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 3.
All (15) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.
Atom-1Atom-2

1:A:165[A]:MET:HE11:A:187:ASP:HA

Interatomic
Clashdistance (Å)
overlap (Å)
1.64
0.78
Continued on next page...

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6Y84

Continued from previous page...
Atom-1Atom-2

1:A:298:ARG:HD2
1:A:197:ASP:HA
1:A:165[A]:MET:CE
1:A:126:TYR:HE1
1:A:298:ARG:HH21
1:A:40:ARG:HA
1:A:294[B]:PHE:CD2
1:A:298:ARG:HG3
1:A:126:TYR:HE1
1:A:294[B]:PHE:CE2
1:A:86[A]:VAL:HG13
1:A:165[A]:MET:SD
1:A:121:SER:HA
1:A:95:ASN:HB3

2:A:403:DMS:H12
3:A:530:HOH:O
1:A:187:ASP:HA
1:A:128[B]:CYS:SG
2:A:403:DMS:H13
1:A:87:LEU:HG
1:A:298:ARG:NH1
1:A:303:VAL:HB
1:A:128[B]:CYS:HG
1:A:298:ARG:NH1
1:A:179:GLY:HA2
1:A:186:VAL:O
1:A:122:PRO:HD3
1:A:98:THR:OG1

Interatomic
distance (Å)
1.81
2.01
2.31
2.27
1.69
1.87
2.74
1.89
1.58
2.79
1.95
2.77
1.92
2.21

Clashoverlap (Å)
0.62
0.60
0.57
0.57
0.56
0.56
0.55
0.54
0.50
0.49
0.49
0.42
0.41
0.40

There are no symmetry-related clashes.

5.3

i
Torsion angles ○

5.3.1

i
Protein backbone ○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 entries
of 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

AllowedOutliers

1A

326/306 (106%)320 (98%)

5 (2%)

1 (0%)

Percentiles
4118All (1) Ramachandran outliers are listed below:
Mol
1Chain
ARes
154

TypeTYR

5.3.2

iProtein sidechains ○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 similar

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6Y84

resolution.
The Analysed column shows the number of residues for which the sidechain conformation wasanalysed, and the total number of residues.
MolChainAnalysed

RotamericOutliers

1A

285/263 (108%)284 (100%)1 (0%)

Percentiles9178All (1) residues with a non-rotameric sidechain are listed below:
Mol
1ChainARes
27

TypeLEU

Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (2) suchsidechains are listed below:
Mol1
1Chain
AARes
19228

5.3.3

i
RNA ○TypeGLNASN

There are no RNA molecules in this entry.

5.4i
Non-standard residues in protein, DNA, RNA chains ○There are no non-standard protein/DNA/RNA residues in this entry.

5.5iCarbohydrates ○There are no monosaccharides in this entry.

5.6iLigand geometry ○4 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. The
Link 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).

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MolTypeChainResLink

2222DMSDMSDMSDMS

A
A
A
A401
404402403-Bond lengths
Counts RMSZ #|Z| > 2
3,3,30.22
03,3,30.33
03,3,30.26
03,3,30.15
0There are no bond length outliers.
There are no bond angle outliers.
There are no chirality outliers.
There are no torsion outliers.
There are no ring outliers.
1 monomer is involved in 2 short contacts:Mol2ChainARes403

TypeDMSClashes
25.7

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

5.8i
Polymer linkage issues ○There are no chain breaks in this entry.

Symm-Clashes
06Y84

Bond angles
Counts RMSZ #|Z| > 2
3,3,30.20
03,3,30.40
03,3,30.40
03,3,30.51
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i
Fit of model and data ○6.1

iProtein, DNA and RNA chains ○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.
MolChainAnalysed<RSRZ>

1A

304/306 (99%)

0.15#RSRZ>214 (4%) 32

32

OWAB(Å2 )Q<0.9

11, 17, 31, 44

2 (0%)All (14) RSRZ outliers are listed below:
Mol11111111111111Chain
A
A
A
A
A
A
A
A
A
A
A
A
A
A

Res
303
304[A]
46
302
73[A]
154
72[A]
294[A]
50
24
168
47
1[A]
23

Type
VAL
THR
SER
GLY
VAL
TYR
ASN
PHE
LEU
THR
PRO
GLU
SER
GLY

RSRZ
6.0
5.2
3.9
3.6
3.5
3.4
3.4
3.3
3.0
2.8
2.6
2.2
2.1
2.0

6.2i
Non-standard residues in protein, DNA, RNA chains ○There are no non-standard protein/DNA/RNA residues in this entry.

6.3

iCarbohydrates ○There are no monosaccharides in this entry.

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iLigands ○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 column
labelled ‘Q< 0.9’ lists the number of atoms with occupancy less than 0.9.
Mol2222TypeDMSDMSDMSDMSChainAAAARes
402
404
403
401

Atoms
4/4
4/4
4/4
4/4

6.5

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

RSCC
0.89
0.91
0.97
0.97

RSR
0.17
0.23
0.16
0.08

B-factors(Å2 )48,48,48,48
36,36,36,36
29,30,30,30
19,19,20,20

Q<0.90000