iFull wwPDB X-ray Structure Validation Report ○Dec 14, 2021 – 04:01 PM ESTPDB ID :Title :
Authors :Deposited on :Resolution :7RFS
Structure of SARS-CoV-2 main protease in complex with a covalent inhibitor
Greasley, S.E.; Ferre, R.A.; Liu, W.; Stewart, A.E.
2021-07-14
1.91 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/XrayValidationReportHelpi symbol.
with specific help available everywhere you see the ○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
Refmac
CCP4
Ideal geometry (proteins)
Ideal geometry (DNA, RNA)
Validation Pipeline (wwPDB-VP)

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:
:
:
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4.02b-467
1.8.5 (274361), CSD as541be (2020)
1.13
2.24
1.1.7 (2018)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)
2.24

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7RFSi
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 1.91 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 ree
Clashscore
Ramachandran outliers
Sidechain outliersRSRZ outliers

Whole archive(#Entries)
130704141614138981138945127900Similar resolution(#Entries, resolution range(Å))
7937 (1.94-1.90)
8644 (1.94-1.90)8530 (1.94-1.90)8530 (1.94-1.90)
7793 (1.94-1.90)

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

Length1

A306

Quality of chain

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7RFSi
Entry composition ○There are 3 unique types of molecules in this entry. The entry contains 2518 atoms, of which 33
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 3C-like proteinase.
MolChainResidues

1A306

Atoms
TotalCN2367 1499 402

O444

S
22

ZeroOcc

AltConfTrace000• Molecule 2 is (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxa
mide (three-letter code: 4WI) (formula: C23 H34 F3 N5 O4 ) (labeled as "Ligand of Interest" bydepositor).

Mol

Chain

Residues

2A

1

Total
68

Atoms
C F H N
23 3 33 5O
4

ZeroOcc

AltConf330• Molecule 3 is water.
Mol

Chain

Residues

3A83

Atoms
Total O83
83

ZeroOcc

AltConf00

Page 43Full wwPDB X-ray Structure Validation Report7RFSiResidue-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 presentin the sample, but not in the model, are shown in grey.
• Molecule 1: 3C-like proteinase

K269

L242

•
N231
L232
V233
A234
M235

•
•
L220
N221
R222
F223

L227

•
R217

A210

I200

•
T169

G179

•
Y154
D155

G149

C145

N142

T135

R131

S121
P122

S113
V114
L115

G109

T98

N95

•
S301 •
G302 •
V303 •
T304 •
F305 •
Q306 •

V86

Q74

D295
V296
V297
R298

R279•F294 •

S1P39

•

Chain A:

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7RFSi
Data 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 )ValueC121
114.20Å 53.03Å 45.68Å
90.00◦ 102.52◦ 90.00◦
55.74 – 1.91
55.74 – 1.91
66.1 (55.74-1.91)
66.1 (55.74-1.91)(Not available)(Not available)
1.05 (at 1.91Å)
BUSTER 2.11.8
0.215 , 0.260
0.205 , 0.250
711 reflections (5.16%)
43.7
0.037
0.38 , 52.0
< |L| > = 0.50, < L2 > = 0.33
No twinning to report.
0.95
2518
48.0

SourceDepositor
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 9.94% 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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Model quality ○5.1iStandard geometry ○Bond lengths and bond angles in the following residue types are not validated in this section:
4WIThe 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 anoutlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (orangles).
MolChain1

A

Bond lengths
RMSZ #|Z| >50.42
0/2420Bond angles
RMSZ #|Z| >50.60
0/3289There are no bond length outliers.
There are no bond angle outliers.
There are no chirality outliers.
There are no planarity outliers.

5.2i
Too-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-H2367
35832485

H(model)
033033H(added)
2313
002313Clashes
180018

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 4.
All (18) close contacts within the same asymmetric unit are listed below, sorted by their clash
magnitude.
Atom-1Atom-2

1:A:231:ASN:O

1:A:235:MET:HG2

Interatomic
Clashdistance (Å)
overlap (Å)
1.83
0.79
Continued on next page...

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

1:A:86:VAL:HG13
1:A:233:VAL:HG11
1:A:298:ARG:CG
1:A:131:ARG:HG2
1:A:109:GLY:HA2
1:A:298:ARG:HG3
1:A:115:LEU:HD11
1:A:298:ARG:HD3
1:A:227:LEU:HD21
1:A:95:ASN:HB3
1:A:155:ASP:HB3
1:A:298:ARG:HG2
1:A:39:PRO:HG2
1:A:121:SER:HA
1:A:217:ARG:HD3
1:A:210:ALA:HB2
1:A:113:SER:O

1:A:179:GLY:HA2
1:A:269:LYS:HG3
1:A:303:VAL:HB
1:A:135:THR:O
1:A:200:ILE:HD13
1:A:303:VAL:HB
1:A:122:PRO:HB3
1:A:305:PHE:HZ
1:A:242:LEU:HD23
1:A:98:THR:OG1
1:A:306:GLN:HG3
1:A:303:VAL:HB
1:A:145:CYS:HB3
1:A:122:PRO:HD3
1:A:220:LEU:HD12
1:A:296:VAL:HG13
1:A:149:GLY:HA2Interatomic
distance (Å)
1.86
1.87
2.38
2.07
1.91
1.93
1.96
1.80
1.98
2.16
2.00
1.99
2.02
1.92
2.03
2.02
2.21

Clashoverlap (Å)
0.58
0.57
0.54
0.53
0.52
0.50
0.47
0.47
0.46
0.45
0.43
0.43
0.42
0.41
0.41
0.41
0.40

There are no symmetry-related clashes.

5.3iTorsion angles ○5.3.1

iProtein 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.
MolChainAnalysed

Favoured

AllowedOutliers

1

A

304/306 (99%)

293 (96%)

10 (3%)

1 (0%)All (1) Ramachandran outliers are listed below:Mol1ChainARes
154

TypeTYRPercentiles
4131

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7RFSiProtein 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
resolution.
The Analysed column shows the number of residues for which the sidechain conformation wasanalysed, and the total number of residues.
MolChainAnalysed

RotamericOutliers

1A

263/263 (100%)

261 (99%)2 (1%)

Percentiles
8181

All (2) residues with a non-rotameric sidechain are listed below:
Mol
11ChainAARes
142294TypeASNPHE

Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. There areno such sidechains identified.
5.3.3

i
RNA ○

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.

5.6

i
Ligand geometry ○1 ligand is 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 thePage 9

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7RFS

expected 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).
MolTypeChainRes

Link

24WIA

401

1

Bond lengths
Counts RMSZ #|Z| > 2
35,37,37
1.54
5 (14%)

Bond angles
Counts RMSZ #|Z| > 2
45,59,59
1.34
6 (13%)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.
Mol2

Type
4WI

ChainARes
401

Link
1

Chirals-Torsions
0/36/73/73

Rings
0/3/3/3

All (5) bond length outliers are listed below:
Mol
22222

ChainA
A
A
A
A

Res
401
401
401
401
401

Type
4WI
4WI
4WI
4WI
4WIAtoms
C8-N2
C12-C9
C21-N4
C10-C11
C15-C14Z
5.03
-3.28
2.57
-2.57
-2.50

Observed(Å)
1.39
1.50
1.39
1.48
1.52

Ideal(Å)
1.33
1.54
1.34
1.52
1.56All (6) bond angle outliers are listed below:Mol
2222
22ChainA
A
A
A
A
A

Res
401
401
401
401
401
401

Type
4WI
4WI
4WI
4WI
4WI
4WIAtoms
C13-C14-N4
C12-C18-C11
C3-C2-N1
C1-C9-N3
C22-C21-N4
C14-C13-N3

Z
-3.53
-2.57
-2.34
-2.21-2.15-2.04

Observed(o )103.4958.61
106.23106.63112.28116.07

Ideal(o )107.3460.15
110.54111.83115.14118.52

There are no chirality outliers.
There are no torsion outliers.
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 isPage 10

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7RFS

within 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 ringin 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 4WI A 401

5.7

Bond lengths

Bond anglesTorsions

Rings

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

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

7RFS

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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>

1A306/306 (100%)

0.14#RSRZ>216 (5%) 2730

OWAB(Å2 )Q<0.932, 46, 69, 89

0All (16) RSRZ outliers are listed below:
Mol1111111111111111Chain
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A

Res
154
305
306
223
222
303
217
294
304
301
233
169
279
302
74
298

Type
TYR
PHE
GLN
PHE
ARG
VAL
ARG
PHE
THR
SER
VAL
THR
ARG
GLY
GLN
ARG

RSRZ
10.7
6.7
4.9
4.9
3.5
3.4
3.3
3.1
2.9
2.8
2.4
2.3
2.3
2.2
2.2
2.1

6.2

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

6.3

i
Carbohydrates ○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.
Mol2Type4WIChainARes401

Atoms
35/35

RSCC
0.90

RSR0.14

B-factors(Å2 )46,50,54,54

Q<0.933

The following is a graphical depiction of the model fit to experimental electron density of all
instances of the Ligand of Interest. In addition, ligands with molecular weight > 250 and outliers
as shown on the geometry validation Tables will also be included. Each fit is shown from different
orientation to approximate a three-dimensional view.

Electron density around 4WI A 401:2mFo -DFc (at 0.7 rmsd) in graymFo -DFc (at 3 rmsd) in purple (negative)
and green (positive)

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

7RFS