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Full wwPDB X-ray Structure Validation Report ○
Feb 12, 2017 – 11:32 pm GMT
PDB ID
Title
Authors
Deposited on
Resolution
:
:
:
:
:
4WN0
Xenopus laevis embryonic epidermal lectin in complex with glycerol phosphate
Wangkanont, K.; Kiessling, L.L.; Forest, K.T.
2014-10-10
2.20 Å(reported)
This is a Full wwPDB X-ray Structure Validation Report for a publicly released PDB entry.
We welcome your comments at [email protected]
A user guide is available at
http://wwpdb.org/validation/2016/XrayValidationReportHelp
i 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
Percentile statistics
Refmac
CCP4
Ideal geometry (proteins)
Ideal geometry (DNA, RNA)
Validation Pipeline (wwPDB-VP)
:
:
:
:
:
:
:
:
:
:
4.02b-467
1.7.2 (RC1), CSD as538be (2017)
1.9-1692
trunk28620
20161228.v01 (using entries in the PDB archive December 28th 2016)
5.8.0135
6.5.0
Engh & Huber (2001)
Parkinson et al. (1996)
recalc28949
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4WN0
i
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 2.20 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.
Metric
Rf ree
Clashscore
Ramachandran outliers
Sidechain outliers
RSRZ outliers
Whole archive
(#Entries)
100719
112137
110173
110143
101464
Similar resolution
(#Entries, resolution range(Å))
4002 (2.20-2.20)
4730 (2.20-2.20)
4656 (2.20-2.20)
4657 (2.20-2.20)
4033 (2.20-2.20)
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. 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.
Mol
Chain
Length
1
A
289
Quality of chain
The following table lists non-polymeric compounds, carbohydrate monomers and non-standard
residues in protein, DNA, RNA chains that are outliers for geometric or electron-density-fit criteria:
Mol
4
4
Type
1PE
1PE
Chain
A
A
Res
405
406
Chirality
-
Geometry
-
Clashes Electron density
X
X
Continued on next page...
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Continued from previous page...
Mol Type Chain Res Chirality
4
1PE
A
407
4
1PE
A
408
-
Geometry
-
Clashes
-
Electron density
X
X
4WN0
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4WN0
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Entry composition ○
There are 6 unique types of molecules in this entry. The entry contains 2400 atoms, of which 0
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 2
atoms.
• Molecule 1 is a protein called XEEL protein.
Mol
Chain
Residues
1
A
277
Atoms
Total
C
N
2151 1348 367
O
422
S
14
ZeroOcc
AltConf
Trace
0
2
0
• Molecule 2 is CALCIUM ION (three-letter code: CA) (formula: Ca).
Mol
Chain
Residues
2
A
3
Atoms
Total Ca
3
3
ZeroOcc
AltConf
0
0
• Molecule 3 is PHOSPHATE ION (three-letter code: PO4) (formula: O4 P).
Mol
Chain
Residues
3
A
1
Atoms
Total O P
5
4 1
ZeroOcc
AltConf
0
0
• Molecule 4 is PENTAETHYLENE GLYCOL (three-letter code: 1PE) (formula: C10 H22 O6 ).
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Full wwPDB X-ray Structure Validation Report
Mol
Chain
Residues
4
A
1
4
A
1
4
A
1
4
A
1
Atoms
Total C
16
10
Total C
16
10
Total C
16
10
Total C
16
10
O
6
O
6
O
6
O
6
ZeroOcc
AltConf
0
0
0
0
0
0
0
0
4WN0
• Molecule 5 is S N - G L Y C E R O L - 3 - P H O S P H A T E (three-letter code: G3P) (formula:
C3 H9 O6 P).
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Full wwPDB X-ray Structure Validation Report
Mol
Chain
Residues
5
A
1
Atoms
Total C O
10
3 6
P
1
ZeroOcc
AltConf
0
0
• Molecule 6 is water.
Mol
Chain
Residues
6
A
167
Atoms
Total O
167 167
ZeroOcc
AltConf
0
0
4WN0
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4WN0
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Residue-property plots ○
These plots are drawn for all protein, RNA and DNA chains in the entry. The first graphic for
a chain summarises the proportions of the various outlier classes displayed in the second graphic.
The second graphic shows the sequence view annotated by issues in geometry and electron 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: XEEL protein
F340
Y341
R342
L315
S305
P306
•
K286
L279
S272
T261
L251
K247
G243
K222
W190
M187
A177
W108
D100
ARG
SER
GLY
GLY
SER
PRO
THR
GLY
ASP
MET
ASN
TYR
G66
•
Chain A:
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4WN0
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Data and refinement statistics ○
Property
Space group
Cell constants
a, b, c, α, β, γ
Resolution (Å)
% Data completeness
(in resolution range)
Rmerge
Rsym
< 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
P6
124.63Å 124.63Å 55.59Å
90.00◦
90.00◦ 120.00◦
29.93 – 2.20
30.20 – 2.20
99.8 (29.93-2.20)
96.7 (30.20-2.20)
(Not available)
0.13
3.47 (at 2.20Å)
PHENIX
0.151 , 0.169
0.144 , 0.167
1258 reflections (4.99%)
29.6
0.267
0.40 , 54.9
< |L| > = 0.49, < L2 > = 0.32
0.043 for h,-h-k,-l
0.97
2400
25.0
Source
Depositor
Depositor
Depositor
EDS
Depositor
EDS
Depositor
Depositor
Xtriage
Depositor
Depositor
DCC
DCC
Xtriage
Xtriage
EDS
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 5.12% 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.
1
2
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4WN0
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Model quality ○
5.1
i
Standard geometry ○
Bond lengths and bond angles in the following residue types are not validated in this section: G3P,
CA, PO4, 1PE
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
0.37
0/2207
Bond angles
RMSZ #|Z| >5
0.54
0/2994
There are no bond length outliers.
There are no bond angle outliers.
There are no chirality outliers.
There are no planarity outliers.
5.2
i
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 hydrogen
atoms 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
2
3
4
5
6
All
Chain
A
A
A
A
A
A
All
Non-H
2151
3
5
64
10
167
2400
H(model)
0
0
0
0
0
0
0
H(added)
2007
0
0
88
5
0
2100
Clashes
10
0
1
7
0
1
12
Symm-Clashes
0
0
0
0
0
0
0
The all-atom clashscore is defined as the number of clashes found per 1000 atoms (including
hydrogen atoms). The all-atom clashscore for this structure is 3.
All (12) close contacts within the same asymmetric unit are listed below, sorted by their clash
magnitude.
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Full wwPDB X-ray Structure Validation Report
Atom-1
Atom-2
3:A:404:PO4:O2
1:A:243:GLY:H
1:A:286:LYS:HD3
1:A:100:ASP:HB3
1:A:261:THR:OG1
4:A:408:1PE:H141
1:A:222:LYS:HD2
1:A:187:MET:HA
1:A:247:LYS:HZ1
1:A:305:SER:HA
1:A:306:PRO:HD2
1:A:177:ALA:HB3
6:A:630:HOH:O
4:A:407:1PE:H152
4:A:406:1PE:H141
1:A:108:TRP:HB2
4:A:406:1PE:H231
4:A:408:1PE:H162
4:A:405:1PE:H242
1:A:190:TRP:CE2
4:A:407:1PE:H222
1:A:306:PRO:HA
4:A:408:1PE:H261
1:A:340:PHE:HB2
Interatomic
distance (Å)
2.18
1.73
1.92
1.92
2.12
1.95
1.97
2.55
1.84
1.78
2.01
2.04
4WN0
Clash
overlap (Å)
0.57
0.53
0.52
0.51
0.49
0.49
0.46
0.42
0.42
0.41
0.41
0.40
There are no symmetry-related clashes.
5.3
5.3.1
i
Torsion angles ○
i
Protein backbone ○
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
277/289 (96%)
265 (96%)
12 (4%)
0
Percentiles
100
100
There are no Ramachandran outliers to report.
5.3.2
i
Protein sidechains ○
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.
Page 11
Full wwPDB X-ray Structure Validation Report
Mol
Chain
Analysed
Rotameric
Outliers
1
A
225/232 (97%)
222 (99%)
3 (1%)
4WN0
Percentiles
73
85
All (3) residues with a non-rotameric sidechain are listed below:
Mol
1
1
1
Chain
A
A
A
Res
251
272
315
Type
LEU
SER
LEU
Some sidechains can be flipped to improve hydrogen bonding and reduce clashes. There are no
such sidechains identified.
5.3.3
i
RNA ○
There are no RNA molecules in this entry.
5.4
i
Non-standard residues in protein, DNA, RNA chains ○
There are no non-standard protein/DNA/RNA residues in this entry.
5.5
i
Carbohydrates ○
There are no carbohydrates in this entry.
5.6
i
Ligand geometry ○
Of 9 ligands modelled in this entry, 3 are monoatomic - leaving 6 for Mogul analysis.
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 and
the 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 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| > 2 is considered an outlier worth inspection. RMSZ is
the root-mean-square of all Z scores of the bond lengths (or angles).
Mol
Type
Chain
Res
Link
3
4
4
PO4
1PE
1PE
A
A
A
404
405
406
-
Bond lengths
Counts RMSZ #|Z| > 2
4,4,4
0.77
0
15,15,15
0.62
0
15,15,15
0.59
0
Bond angles
Counts RMSZ #|Z| > 2
6,6,6
0.39
0
14,14,14
0.84
0
14,14,14
0.89
0
Page 12
Full wwPDB X-ray Structure Validation Report
Mol
Type
Chain
Res
Link
4
4
5
1PE
1PE
G3P
A
A
A
407
408
409
2
Bond lengths
Counts RMSZ #|Z| > 2
15,15,15
0.62
0
15,15,15
0.65
0
9,9,9
1.55
2 (22%)
4WN0
Bond angles
Counts RMSZ #|Z| > 2
14,14,14
0.92
0
14,14,14
0.77
0
11,12,12
1.18
1 (9%)
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 the chemical
component dictionary. Similar counts are reported in the Torsion and Rings columns. ’-’ means
no outliers of that kind were identified.
Mol
3
4
4
4
4
5
Type
PO4
1PE
1PE
1PE
1PE
G3P
Chain
A
A
A
A
A
A
Res
404
405
406
407
408
409
Link
2
Chirals
-
Torsions
0/0/0/0
0/13/13/13
0/13/13/13
0/13/13/13
0/13/13/13
0/8/8/8
Rings
0/0/0/0
0/0/0/0
0/0/0/0
0/0/0/0
0/0/0/0
0/0/0/0
All (2) bond length outliers are listed below:
Mol
5
5
Chain
A
A
Res
409
409
Type
G3P
G3P
Atoms
P-O4P
P-O2P
Z
2.00
3.75
Observed(Å)
1.63
1.63
Ideal(Å)
1.54
1.50
All (1) bond angle outliers are listed below:
Mol
5
Chain
A
Res
409
Type
G3P
Atoms
O3P-P-O1P
Z
2.81
Observed(o )
114.21
There are no chirality outliers.
There are no torsion outliers.
There are no ring outliers.
5 monomers are involved in 8 short contacts:
Mol
3
4
4
4
4
Chain
A
A
A
A
A
Res
404
405
406
407
408
Type
PO4
1PE
1PE
1PE
1PE
Clashes
1
1
2
2
2
Symm-Clashes
0
0
0
0
0
Ideal(o )
106.73
Page 13
5.7
Full wwPDB X-ray Structure Validation Report
i
Other polymers ○
There are no such residues in this entry.
5.8
i
Polymer linkage issues ○
There are no chain breaks in this entry.
4WN0
Page 14
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4WN0
i
Fit of model and data ○
6.1
i
Protein, 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 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
277/289 (95%)
-0.55
#RSRZ>2
2 (0%) 87
86
OWAB(Å2 )
Q<0.9
15, 23, 34, 51
0
All (2) RSRZ outliers are listed below:
Mol
1
1
6.2
Chain
A
A
Res
66
279
Type
GLY
LEU
RSRZ
3.8
2.1
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 carbohydrates in this entry.
6.4
i
Ligands ○
In the following table, the Atoms column lists the number of modelled atoms in the group and the
number defined in the chemical component dictionary. LLDF column lists the quality of electron
density of the group with respect to its neighbouring residues in protein, DNA or RNA chains.
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.
Mol
4
4
4
Type
1PE
1PE
1PE
Chain
A
A
A
Res
408
407
405
Atoms
16/16
16/16
16/16
RSCC
0.84
0.79
0.84
RSR
0.42
0.38
0.26
LLDF
30.08
13.13
9.65
B-factors(Å2 ) Q<0.9
45,51,65,67
0
44,51,62,63
0
47,53,61,66
0
Continued on next page...
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Continued from previous page...
Mol Type Chain Res Atoms
4
1PE
A
406
16/16
5
G3P
A
409
10/10
2
CA
A
402
1/1
2
CA
A
401
1/1
2
CA
A
403
1/1
3
PO4
A
404
5/5
6.5
i
Other polymers ○
There are no such residues in this entry.
RSCC
0.72
0.84
0.99
0.99
0.99
0.79
RSR
0.28
0.14
0.07
0.04
0.03
0.35
LLDF
2.98
0.92
-1.19
-2.18
-3.80
-
B-factors(Å2 )
46,52,63,64
21,30,52,65
15,15,15,15
15,15,15,15
20,20,20,20
61,67,82,83
4WN0
Q<0.9
0
0
0
0
0
0