iFull wwPDB X-ray Structure Validation Report ○Nov 19, 2023 – 05:49 PM JST
PDB ID
TitleAuthors
Deposited onResolution:::::

6LVN
Structure of the 2019-nCoV HR2 Domain
Zhu, Y.; Sun, F.
2020-02-04
2.47 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
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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6LVNi
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 2.47 Å.
Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown inthe 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)
130704141614138981138945127900

Similar resolution(#Entries, resolution range(Å))
5857 (2.50-2.46)
6594 (2.50-2.46)6469 (2.50-2.46)
6471 (2.50-2.46)
5738 (2.50-2.46)

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

Length

1

A36

1

B

36

1

C36

1

D36

Quality of chain

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6LVNiEntry composition ○There are 2 unique types of molecules in this entry. The entry contains 1078 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 Spike protein S2’.
MolChainResidues

1A

34

1

B35

1

C33

1

D34

Atoms
Total CN
264 162 46
Total CN
272 168 47
Total CN256 156 45
Total CN
264 162 46

O56
O57
O55
O56

ZeroOcc

AltConfTrace000000000000• Molecule 2 is water.
MolChainResidues

2A62B

92C52D2Atoms
Total O
66Total O
99Total O
55Total O
22ZeroOcc

AltConf00000000

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6LVN

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 2
or 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: Spike protein S2’

E35LEUASP
I2
S3

Chain A:• Molecule 1: Spike protein S2’

L36

ASP
I2S3•

Chain B:

• Molecule 1: Spike protein S2’

E35
LEU

E28

K24

K14

V9ASPILE
S3G4I5N6Chain C:• Molecule 1: Spike protein S2’

E35LEU

L26
N27
E28
S29
L30
I31

R18

K14

ASP
I2
S3

•

Chain D:

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6LVN

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
P 21 21 21
28.20Å 49.73Å 89.58Å
90.00◦ 90.00◦ 90.00◦
25.60 – 2.47
26.89 – 2.47
99.3 (25.60-2.47)
99.3 (26.89-2.47)
0.13(Not available)
2.57 (at 2.47Å)PHENIX
0.215 , 0.258
0.217 , 0.256
290 reflections (5.96%)
29.9
0.528
0.36 , 46.9
< |L| > = 0.49, < L2 > = 0.34
No twinning to report.
0.94
1078
38.0Source
Depositor
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 15.53% 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 ○5.1

iStandard 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).
MolChain1111AllABCDAll

Bond lengths
RMSZ #|Z| >50.29
0/263
0.28
0/271
0.30
0/255
0.37
0/263
0.31
0/1052

Bond angles
RMSZ #|Z| >50.38
0/354
0.40
0/365
0.41
0/343
0.64
0/354
0.47
0/1416

There 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.
Mol
1
1
1
12
2
22AllChainABCDA
BCDAllNon-H
264
272
256
264
6
952
1078

H(model)
000000000H(added)
270
281
259
27000001080

Clashes014300008Symm-Clashes
000000000

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.

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6LVN

All (8) close contacts within the same asymmetric unit are listed below, sorted by their clash
magnitude.
Atom-1Atom-2

1:C:5:ILE:O
1:D:26:LEU:O
1:D:28:GLU:HA
1:C:24:LYS:O
1:B:2:ILE:HG23
1:C:6:ASN:O
1:C:14:LYS:HB3
1:D:14:LYS:HD3

1:C:9:VAL:HG13
1:D:30:LEU:HD13
1:D:31:ILE:HG13
1:C:28:GLU:HG3
1:B:3:SER:H
1:C:9:VAL:HG22
1:C:14:LYS:HE3
1:D:18:ARG:NH2Interatomicdistance (Å)
2.02
2.07
1.89
2.10
1.76
2.13
1.74
2.34

Clashoverlap (Å)
0.58
0.55
0.55
0.51
0.50
0.49
0.44
0.43

There are no symmetry-related clashes.

5.3

iTorsion 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 entriesof 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

Percentiles

1A

32/36 (89%)

32 (100%)

00100

1001

B

33/36 (92%)

33 (100%)

00100

100

1C

31/36 (86%)

30 (97%)

1 (3%)

0100

1001D

32/36 (89%)

32 (100%)

00100

100AllAll

128/144 (89%)

127 (99%)1 (1%)

0100

100

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 8Full wwPDB X-ray Structure Validation Report

6LVN

analysed, and the total number of residues.
MolChainAnalysed

RotamericOutliers

Percentiles

1A

31/33 (94%)

30 (97%)

1 (3%)

3963

1B

32/33 (97%)

32 (100%)

0100

100

1C

30/33 (91%)

30 (100%)

0100100

1D

31/33 (94%)

30 (97%)

1 (3%)

3963AllAll

124/132 (94%)

122 (98%)

2 (2%)

6282

All (2) residues with a non-rotameric sidechain are listed below:
Mol
11Chain
ADRes
33TypeSER
SER

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 ○There are no ligands in this entry.

5.7

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

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

6LVN

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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>#RSRZ>2OWAB(Å2 )Q<0.91A

34/36 (94%)

-0.29

0 100

24, 33, 50, 72

01B

35/36 (97%)-0.23

1 (2%) 5123, 32, 48, 56

01

C

33/36 (91%)

-0.19

0 100

27, 35, 65, 75

01

D34/36 (94%)

0.17

1 (2%) 51

54

25, 40, 61, 78

0All

All

136/144 (94%)-0.13

2 (1%) 73

75

23, 34, 62, 78

0100
54100

All (2) RSRZ outliers are listed below:
Mol1
1ChainDB

Res
236

TypeILE
LEU

RSRZ
5.5
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

iLigands ○There are no ligands in this entry.

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