iFull wwPDB X-ray Structure Validation Report ○Nov 21, 2023 – 05:54 PM JST
PDB ID
TitleAuthors
Deposited onResolution:::::

6M03
The crystal structure of COVID-19 main protease in apo form
Zhang, B.; Zhao, Y.; Jin, Z.; Liu, X.; Yang, H.; Rao, Z.
2020-02-19
2.00 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 ○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
Xtriage (Phenix)
EDS
Percentile statistics
Refmac
CCP4
Ideal geometry (proteins)
Ideal geometry (DNA, RNA)
Validation Pipeline (wwPDB-VP)

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4.02b-467
1.13
2.36
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)
2.36

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6M03

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 2.00 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 outliers
RSRZ outliers

Whole archive(#Entries)
130704141614138981138945127900Similar resolution(#Entries, resolution range(Å))
8085 (2.00-2.00)
9178 (2.00-2.00)
9054 (2.00-2.00)
9053 (2.00-2.00)
7900 (2.00-2.00)

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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6M03

iEntry composition ○There are 2 unique types of molecules in this entry. The entry contains 2454 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.
Mol

Chain

Residues

1A

306

Atoms
TotalCN
2367 1499 402

O444

S
22

ZeroOcc

AltConfTrace000• Molecule 2 is water.
MolChainResidues

2A87Atoms
Total O
8787

ZeroOcc

AltConf00

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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

F305
Q306

••

•
•
•
S301
G302
V303
T304

V296

R279

M235

N231

N221
R222
F223

R217
W218

A210

T169
G170
V171

D153
Y154
D155

G149

S113

T98

N95

V86
L87

Q83

V68
Q69
A70G71
N72
V73

D48

T45

R40

V36

S1G2•

Chain A:

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6M03i
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 )

Value
C121
113.96Å 53.45Å 45.03Å
90.00◦ 101.83◦ 90.00◦
38.65 – 2.00
48.20 – 1.99
99.7 (38.65-2.00)
94.6 (48.20-1.99)
0.04(Not available)
1.23 (at 2.00Å)PHENIX 1.12_2829
0.196 , 0.246
0.197 , 0.247
1829 reflections (10.00%)
39.2
0.203
0.34 , 48.1
< |L| > = 0.50, < L2 > = 0.33
No twinning to report.
0.96
2454
52.0

SourceDepositor
Depositor
Depositor
EDS
Depositor
EDS
Depositor
Depositor
Xtriage
Depositor
DepositorDCC
wwPDB-VP
Xtriage
Xtriage
EDSXtriageXtriageEDS
wwPDB-VP
wwPDB-VP

Xtriage’s analysis on translational NCS is as follows: The largest off-origin peak in the Patterson function is 10.42% 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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6M03iModel quality ○5.1iStandard geometry ○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 anoutlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (orangles).
Mol

Chain

1A

Bond lengths
RMSZ #|Z| >50.27
0/2420Bond angles
RMSZ #|Z| >50.50
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.
Mol12All

ChainAAAll

Non-H2367
872454H(model)000H(added)
2314
02314

Clashes19019Symm-Clashes
000The 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 (19) close contacts within the same asymmetric unit are listed below, sorted by their clash
magnitude.
Atom-1Atom-2

1:A:154:TYR:H
1:A:69:GLN:HE21
1:A:1:SER:OG
1:A:169:THR:OG1

1:A:305:PHE:HD1
1:A:72:ASN:HA
1:A:2:GLY:N
1:A:171:VAL:HG22

Interatomic
Clashdistance (Å)
overlap (Å)
1.46
0.64
1.71
0.56
2.42
0.52
2.09
0.52
Continued on next page...

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6M03

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

1:A:95:ASN:HB3
1:A:40:ARG:HA
1:A:70:ALA:O
1:A:36:VAL:HG21
1:A:153:ASP:CG
1:A:231:ASN:HB3
1:A:231:ASN:O
1:A:113:SER:O
1:A:231:ASN:O
1:A:221:ASN:ND2
1:A:155:ASP:OD1
1:A:218:TRP:HB2
1:A:83:GLN:O
1:A:45:THR:H
1:A:210:ALA:HB2

1:A:98:THR:OG1
1:A:87:LEU:HG
1:A:73:VAL:HG22
1:A:68:VAL:HG11
1:A:153:ASP:O
1:A:235:MET:CE
1:A:235:MET:HE21:A:149:GLY:HA2
1:A:235:MET:CE
1:A:223:PHE:HB2
1:A:155:ASP:N
1:A:279:ARG:HH22
1:A:86:VAL:HG12
1:A:48:ASP:HB2
1:A:296:VAL:HG13

Interatomicdistance (Å)
2.11
1.93
2.12
1.97
2.54
2.45
2.17
2.17
2.66
2.32
2.51
1.84
2.19
1.85
2.03

Clashoverlap (Å)
0.51
0.49
0.49
0.47
0.46
0.45
0.45
0.44
0.44
0.44
0.43
0.43
0.42
0.40
0.40

There are no symmetry-related clashes.

5.3i
Torsion angles ○5.3.1iProtein 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

1A

304/306 (99%)

294 (97%)

10 (3%)

0Percentiles
100100

There are no Ramachandran outliers to report.
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
resolution.
The Analysed column shows the number of residues for which the sidechain conformation wasPage 8

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6M03

analysed, and the total number of residues.
MolChainAnalysed

RotamericOutliers

1

A

263/263 (100%)

260 (99%)

3 (1%)

Percentiles
7378

All (3) residues with a non-rotameric sidechain are listed below:Mol11
1ChainAAARes217
222
235

TypeARG
ARG
METSometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (3) suchsidechains are listed below:
Mol111ChainAAARes6972
203

5.3.3

iRNA ○TypeGLNASN
ASN

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 ○There are no ligands in this entry.

5.7

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

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

6M03

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iFit 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.
Mol

ChainAnalysed<RSRZ>

1A

306/306 (100%)-0.07#RSRZ>26 (1%) 6563

OWAB(Å2 )Q<0.931, 50, 77, 99

0All (6) RSRZ outliers are listed below:
Mol111111ChainAAA
A
A
ARes
154
306
305
303
302
301

TypeTYR
GLNPHEVALGLYSERRSRZ
5.6
4.2
4.0
3.2
2.9
2.5

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.

6.4

i
Ligands ○There are no ligands in this entry.

6.5iOther polymers ○There are no such residues in this entry.