iFull wwPDB NMR Structure Validation Report ○Aug 20, 2022 – 09:29 AM EDTPDB ID : 2FXPTitle : Solution Structure of the SARS-Coronavirus HR2 DomainAuthors : Caffrey, M.; Hakansson-McReynolds, S.; Jiang, S.
Deposited on : 2006-02-06
This is a Full wwPDB NMR 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/NMRValidationReportHelpi 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
Percentile statistics
RCI
PANAV
ShiftChecker
Ideal geometry (proteins)
Ideal geometry (DNA, RNA)
Validation Pipeline (wwPDB-VP)

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4.02b-467
20191225.v01 (using entries in the PDB archive December 25th 2019)v_1n_11_5_13_A (Berjanski et al., 2005)
Wang et al. (2010)
2.29
Engh & Huber (2001)Parkinson et al. (1996)
2.29

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Overall quality at a glance ○The following experimental techniques were used to determine the structure:
SOLUTION NMR
The overall completeness of chemical shifts assignment was not calculated.
There are no overall percentile quality scores available for this entry.
The table below summarises the geometric issues observed across the polymeric chains and theirfit to the experimental data. The red, orange, yellow and green segments indicate the fractionof residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria. A cyansegment indicates the fraction of residues that are not part of the well-defined cores, and 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%MolChain

Length1

A55

1

B55

1

C

55

Quality of chain

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Ensemble composition and analysis ○This entry contains 1 models. Identification of well-defined residues and clustering analysis arenot possible.

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2FXPiEntry composition ○There is only 1 type of molecule in this entry. The entry contains 2562 atoms, of which 1278 arehydrogens and 0 are deuteriums.
• Molecule 1 is a protein called Spike glycoprotein.
MolChainResidues

1A

55

1

B55

1

C55

Total
854
Total
854
Total
854

Atoms
CH
264 426CH
264 426CH
264 426

N72
N72
N72

O92
O92
O92

Trace000

There are 6 discrepancies between the modelled and reference sequences:ChainAABBCCResidue
121212Modelled
GLYSER
GLYSER
GLY
SER

Actual-Comment
cloning artifact
cloning artifact
cloning artifact
cloning artifact
cloning artifact
cloning artifact

Reference
UNP P59594
UNP P59594
UNP P59594
UNP P59594
UNP P59594
UNP P59594

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Residue-property plots ○These plots are provided for all protein, RNA, DNA and oligosaccharide chains in the entry. The
first graphic is the same as shown in the summary in section 1 of this report. The second graphic
shows the sequence where residues are colour-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. Stretches of 2 or more consecutive residues without any outliers are shown as green
connectors. Residues which are classified as ill-defined in the NMR ensemble, are shown in cyanwith an underline colour-coded according to the previous scheme. Residues which were present inthe experimental sample, but not modelled in the final structure are shown in grey.
• Molecule 1: Spike glycoprotein

G1S2H3T4S5P6
D7V8D9L10G11
D12I13
S14G15
I16
N17A18
S19
V20
V21
N22
I23
Q24
K25
E26
I27
D28
R29
L30
N31
E32
V33
A34
K35
N36
L37
N38
E39
S40
L41
I42
D43
L44Q45
E46
L47
G48
K49
Y50
E51
Q52
Y53
I54
K55

Chain A:• Molecule 1: Spike glycoprotein

G1S2
H3T4S5P6
D7V8
D9L10G11
D12I13
S14G15
I16
N17A18
S19
V20
V21N22I23
Q24
K25
E26
I27
D28R29
L30
N31
E32
V33
A34
K35
N36L37
N38
E39
S40
L41
I42
D43L44Q45
E46L47
G48
K49
Y50
E51Q52
Y53
I54K55Chain B:

• Molecule 1: Spike glycoprotein

G1
S2
H3
T4
S5P6
D7V8
D9L10G11
D12
I13
S14
G15
I16
N17
A18
S19
V20
V21
N22
I23
Q24
K25
E26
I27
D28
R29
L30
N31
E32
V33
A34
K35
N36
L37
N38
E39
S40
L41
I42
D43
L44
Q45
E46
L47
G48
K49
Y50
E51Q52
Y53
I54K55Chain C:Page 6

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Refinement protocol and experimental data overview ○The models were refined using the following method: torsion angle dynamics.
Of the ? calculated structures, 1 were deposited, based on the following criterion: ?.
The following table shows the software used for structure solution, optimisation and refinement.
Software nameCNSCNSClassification
structure solution
refinement

No chemical shift data was provided.

Version
1.0
1.0

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iModel quality ○6.1iStandard geometry ○There are no covalent bond-length or bond-angle outliers.
There are no bond-length outliers.
There are no bond-angle outliers.
There are no chirality outliers.
There are no planarity outliers.

6.2

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 each chain respectively. The H(added) column lists the number of hydrogenatoms added and optimized by MolProbity. The Clashes column lists the number of clashes
averaged over the ensemble.
Mol111AllChainABCAllNon-H0000H(model)
0000H(added)
0000Clashes
000-

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 -.
There are no clashes.

6.3

i
Torsion angles ○6.3.1

iProtein backbone ○In the following table, the Percentiles column shows the percent Ramachandran outliers of the chain
as a percentile score with respect to all PDB entries followed by that with respect to all NMRentries. The Analysed column shows the number of residues for which the backbone conformation
was analysed and the total number of residues.
Mol111AllChainABCAll

Analysed
0000

Favoured-

Allowed-Outliers-Percentiles-

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There are no Ramachandran outliers.
6.3.2

iProtein sidechains ○In the following table, the Percentiles column shows the percent sidechain outliers of the chain
as a percentile score with respect to all PDB entries followed by that with respect to all NMR
entries. The Analysed column shows the number of residues for which the sidechain conformation
was analysed and the total number of residues.
Mol111AllChainABCAll

Analysed
0000

Rotameric-Outliers-

Percentiles-

There are no protein residues with a non-rotameric sidechain to report.
6.3.3

i
RNA ○

There are no RNA molecules in this entry.

6.4

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

6.5

iCarbohydrates ○There are no monosaccharides in this entry.

6.6i
Ligand geometry ○There are no ligands in this entry.

6.7

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

6.8

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

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Chemical shift validation ○No chemical shift data were provided

2FXP