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Full wwPDB X-ray Structure Validation Report
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May 11, 2015 – 01:29 PM EDT
PDB ID : 4YUO
Title : High-resolution multiconformer synchrotron model of CypA at 273 K
Authors : Keedy, D.A.; Kenner, L.R.; Warkentin, M.; Woldeyes, R.A.; Thompson, M.C.;
Brewster, A.S.; Van Benschoten, A.H.; Baxter, E.L.; Hopkins, J.B.; Uervirojnangkoorn, M.; McPhillips, S.E.; Song, J.; Mori, R.A.; Holton, J.M.; Weis,
W.I.; Brunger, A.T.; Soltis, M.; Lemke, H.; Gonzalez, A.; Sauter, N.K.; Cohen,
A.E.; van den Bedem, H.; Thorne, R.E.; Fraser, J.S.
Deposited on : 2015-03-18
Resolution : 1.20 ˚
A(reported)
This is a full wwPDB validation report for a publicly released PDB entry.
We welcome your comments at validation@mail.wwpdb.org
A user guide is available at http://wwpdb.org/ValidationPDFNotes.html
The following versions of software and data (see references) were used in the production of this report:
MolProbity
Mogul
Xtriage (Phenix)
EDS
Percentile statistics
Refmac
CCP4
Ideal geometry (proteins)
Ideal geometry (DNA, RNA)
Validation Pipeline (wwPDB-VP)
:
:
:
:
:
:
:
:
:
:
4.02b-467
1.17 November 2013
dev-1439
stable24195
21963
5.8.0049
6.1.3
Engh & Huber (2001)
Parkinson et. al. (1996)
stable24195
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Full wwPDB X-ray Structure Validation Report
Overall quality at a glance
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4YUO
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The reported resolution of this entry is 1.20 ˚
A.
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.
Metric
Rf ree
Clashscore
Ramachandran outliers
Sidechain outliers
RSRZ outliers
Whole archive
(#Entries)
66092
79885
78287
78261
66119
Similar resolution
(#Entries, resolution range(˚
A))
1038 (1.26-1.14)
1158 (1.26-1.14)
1106 (1.26-1.14)
1104 (1.26-1.14)
1038 (1.26-1.14)
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 on the lower bar indicate the
fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria.
The upper red bar (where present) indicates the fraction of residues that have poor fit to the
electron density.
Mol
1
Chain
A
Length
165
Quality of chain
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Entry composition
4YUO
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There are 2 unique types of molecules in this entry. The entry contains 4335 atoms, of which 2100
are hydrogens and 0 are deuterium.
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 2
atoms.
Molecule 1 is a protein called Peptidyl-prolyl cis-trans isomerase A.
Mol
Chain
Residues
1
A
163
Total
4151
Atoms
C
H
N
1326 2100 347
O
363
S
15
Molecule 2 is water.
Mol
Chain
Residues
2
A
160
Atoms
Total O
184 184
ZeroOcc
AltConf
0
39
ZeroOcc
AltConf
Trace
0
119
0
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Residue-property plots
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These plots are drawn for all protein, RNA and DNA chains in the entry. The first graphic for a
chain summarises the proportions of errors displayed in the second graphic. The second graphic
shows the sequence view annotated by issues in geometry and electron density. Residues are colorcoded 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: Peptidyl-prolyl cis-trans isomerase A
L164
GLU
K155
N149
•
K133
E134
K125
F113
N108
L98
S99
K82
K44
V29
MET
V2
•
Chain A:
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Data and refinement statistics
Property
Space group
Cell constants
a, b, c, α, β, γ
Resolution (˚
A)
% Data completeness
(in resolution range)
Rmerge
Rsym
< I/σ(I) > 1
Refinement program
R, Rf ree
Rf ree test set
Wilson B-factor (˚
A2 )
Anisotropy
Bulk solvent ksol (e/˚
A3 ), Bsol (˚
A2 )
Estimated twinning fraction
L-test for twinning
Outliers
Fo ,Fc correlation
Total number of atoms
Average B, all atoms (˚
A2 )
4YUO
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Value
P 21 21 21
˚
42.90A 52.43˚
A 89.11˚
A
◦
90.00
90.00◦ 90.00◦
45.19 – 1.20
45.19 – 1.20
91.3 (45.19-1.20)
91.3 (45.19-1.20)
0.11
(Not available)
5.85 (at 1.20˚
A)
PHENIX (phenix.refine: 1.9 1692)
0.127 , 0.146
0.128 , 0.150
1998 reflections (3.44%)
15.2
0.197
0.39 , 42.4
No twinning to report.
< |L| > = 0.48, < L2 > = 0.31
0 of 58119 reflections
0.98
4335
21.0
Source
Depositor
Depositor
Depositor
EDS
Depositor
EDS
Depositor
Depositor
Xtriage
Depositor
Depositor
DCC
DCC
Xtriage
Xtriage
EDS
Xtriage
Xtriage
Xtriage
EDS
wwPDB-VP
wwPDB-VP
Xtriage’s analysis on translational NCS is as follows: The largest off-origin peak in the Patterson
function is 6.84% of the height of the origin peak. No significant pseudotranslation is detected.
1
Intensities estimated from amplitudes.
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Model quality
5.1
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Standard geometry
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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 (or
angles).
Mol
Chain
1
A
Bond lengths
RMSZ #|Z| >5
0.46
0/2400
Bond angles
RMSZ #|Z| >5
0.63
0/3216
There are no bond length outliers.
There are no bond angle outliers.
There are no chirality outliers.
There are no planarity outliers.
5.2
Close contacts
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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 hydrogens
added by MolProbity. The Clashes column lists the number of clashes within the asymmetric unit,
and the number in parentheses is this value normalized per 1000 atoms of the molecule in the
chain. The Symm-Clashes column gives symmetry related clashes, in the same way as for the
Clashes column.
Mol
1
2
All
Chain
A
A
All
Non-H
2051
184
2235
H(model)
2100
0
2100
H(added)
1861
0
1861
Clashes
4
1
4
Symm-Clashes
3
3
4
Clashscore is defined as the number of clashes calculated for the entry per 1000 atoms (including
hydrogens) of the entry. The overall clashscore for this entry is 1.
All (4) close contacts within the same asymmetric unit are listed below.
Atom-1
1:A:82[A]:LYS:HA
1:A:44[B]:LYS:NZ
1:A:99[A]:SER:HB3
Atom-2
1:A:108[A]:ASN:O
2:A:204:HOH:O
1:A:113[A]:PHE:CZ
˚)
Distance(A
2.17
2.47
2.51
˚)
Clash(A
0.45
0.45
0.44
All (4) symmetry-related close contacts are listed below. The label for Atom-2 includes the sym-
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4YUO
metry operator and encoded unit-cell translations to be applied.
Atom-1
2:A:228:HOH:O
1:A:134[A]:GLU:OE1
1:A:149[B]:ASN:HD22
1:A:125[A]:LYS:HZ1
5.3
5.3.1
Atom-2
2:A:270:HOH:O[4 455]
1:A:155[A]:LYS:HZ2[3 545]
2:A:225[B]:HOH:O[4 455]
2:A:286[A]:HOH:O[4 455]
Torsion angles
Distance(˚
A)
2.19
1.68
2.08
2.15
Clash(˚
A)
0.01
-0.08
-0.48
-0.55
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In the following table, the Percentiles column shows the percent Ramachandran outliers of the
chain 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 was
analysed, and the total number of residues.
Mol
Chain
Analysed
Favoured
Allowed
Outliers
1
A
300/165 (182%)
286 (95%)
14 (5%)
0
Percentiles
100
100
There are no Ramachandran outliers to report.
5.3.2
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In the following table, the Percentiles column shows the percent sidechain outliers of the chain
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 sidechain
conformation was analysed, and the total number of residues.
Mol
Chain
Analysed
Rotameric
Outliers
1
A
251/133 (189%)
250 (100%)
1 (0%)
Percentiles
95
81
All (1) residues with a non-rotameric sidechain are listed below:
Mol
1
Chain
A
Res
29
Type
VAL
Some sidechains can be flipped to improve hydrogen bonding and reduce clashes. There are no
such sidechains identified.
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5.3.3
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4YUO
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RNA i
There are no RNA chains in this entry.
5.4
Non-standard residues in protein, DNA, RNA chains
There are no non-standard protein/DNA/RNA residues in this entry.
5.5
Carbohydrates
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There are no carbohydrates in this entry.
5.6
Ligand geometry
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There are no ligands in this entry.
5.7
Other polymers
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There are no such residues in this entry.
5.8
Polymer linkage issues
There are no chain breaks in this entry.
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Fit of model and data
6.1
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Protein, DNA and RNA chains
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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 to
all 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 per
residue. The column labelled ‘Q< 0.9’ lists the number of (and percentage) of residues with an
average occupancy less than 0.9.
Mol
Chain
Analysed
<RSRZ>
1
A
163/165 (98%)
-0.18
#RSRZ>2
2 (1%) 75
81
˚2 )
OWAB(A
Q<0.9
12, 17, 28, 44
0
All (2) RSRZ outliers are listed below:
Mol
1
1
6.2
Chain
A
A
Res
2
133[A]
Type
VAL
LYS
RSRZ
5.7
2.0
Non-standard residues in protein, DNA, RNA chains
There are no non-standard protein/DNA/RNA residues in this entry.
6.3
Carbohydrates
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There are no carbohydrates in this entry.
6.4
Ligands
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There are no ligands in this entry.
6.5
Other polymers
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There are no such residues in this entry.
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