wwPDB X-ray Structure Validation Summary Report
O
i
Aug 29, 2016 04:19 PM EDT
PDB ID
Title
:
:
Authors
Deposited on
Resolution
:
:
:
5EFN
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2
(H574A) in complex with histone H4 Lys6 tripeptide substrate
Hai, Y.; Christianson, D.W.
2015-10-24
1.80 Å(reported)
This is a wwPDB X-ray Structure Validation Summary Report for a publicly released PDB entry.
We welcome your comments at validation@mail.wwpdb.org
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O
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)
:
:
:
:
:
:
:
:
:
:
O) were used in the production of this report:
i
4.02b-467
1.7.1 (RC1), CSD as537be (2016)
1.9-1692
rb-20027939
20151230.v01 (using entries in the PDB archive December 30th 2015)
5.8.0135
6.5.0
Engh & Huber (2001)
Parkinson et al. (1996)
rb-20027939
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wwPDB X-ray Structure Validation Summary Report
1 Overall quality at a glance
O
5EFN
i
The following experimental techniques were used to determine the structure:
X-RAY DIFFRACTION
The reported resolution of this entry is 1.80 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)
91344
102246
100387
100360
91569
Similar resolution
(#Entries, resolution range(Å))
4533
5383
5320
5319
4547
(1.80-1.80)
(1.80-1.80)
(1.80-1.80)
(1.80-1.80)
(1.80-1.80)
The table below summarises the geometric issues observed across the polymeric chains and their t
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 t to the
electron density. The numeric value is given above the bar.
Mol Chain Length
1
A
364
1
B
364
2
E
3
2
F
3
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-t crite-
Page 3
wwPDB X-ray Structure Validation Summary Report
5EFN
ria:
Mol Type Chain Res Chirality Geometry Clashes Electron density
6
MCM
F
101
-
-
-
X
Page 4
wwPDB X-ray Structure Validation Summary Report
2 Entry composition
5EFN
O
i
There are 7 unique types of molecules in this entry. The entry contains 6396 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.
ˆ Molecule 1 is a protein called Hdac6 protein.
Mol Chain Residues
1
B
357
1
A
357
Total
2844
Total
2830
Atoms
C
1796
C
1781
N
502
N
504
O
527
O
527
S
19
S
18
ZeroOcc AltConf Trace
0
13
0
0
11
0
There are 12 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual
B
B
B
B
B
B
A
A
A
A
A
A
435
436
437
438
439
574
435
436
437
438
439
574
SER
ASN
ALA
GLY
GLY
ALA
SER
ASN
ALA
GLY
GLY
ALA
Comment
HIS
HIS
expression tag
expression tag
expression tag
expression tag
expression tag
engineered mutation
expression tag
expression tag
expression tag
expression tag
expression tag
engineered mutation
Reference
UNP
UNP
UNP
UNP
UNP
UNP
UNP
UNP
UNP
UNP
UNP
UNP
A7YT55
A7YT55
A7YT55
A7YT55
A7YT55
A7YT55
A7YT55
A7YT55
A7YT55
A7YT55
A7YT55
A7YT55
ˆ Molecule 2 is a protein called histone H4 tripeptide.
Mol Chain Residues
2
F
3
2
E
3
Total
22
Total
22
Atoms
C
13
C
13
N
4
N
4
O
5
O
5
ZeroOcc AltConf Trace
0
0
0
0
0
0
ˆ Molecule 3 is ZINC ION (three-letter code: ZN) (formula: Zn).
Page 5
wwPDB X-ray Structure Validation Summary Report
Mol Chain Residues
3
B
1
3
A
1
Atoms
Total
1
Total
1
5EFN
ZeroOcc AltConf
Zn
1
Zn
1
0
0
0
0
ˆ Molecule 4 is POTASSIUM ION (three-letter code: K) (formula: K).
Mol Chain Residues
4
B
2
4
A
2
Atoms
Total
2
Total
2
K
2
K
2
ZeroOcc AltConf
0
0
0
0
ˆ Molecule 5 is 1,2-ETHANEDIOL (three-letter code: EDO) (formula: C H O ).
2
Mol Chain Residues
5
B
1
5
B
1
5
A
1
Atoms
Total
4
Total
4
Total
4
C
2
C
2
C
2
O
2
O
2
O
2
6
2
ZeroOcc AltConf
0
0
0
0
0
0
ˆ Molecule 6 is 7-AMINO-4-METHYL-CHROMEN-2-ONE (three-letter code:
(formula: C10 H9 NO2 ).
MCM)
Page 6
wwPDB X-ray Structure Validation Summary Report
Mol Chain Residues
6
F
1
6
E
1
ˆ Molecule 7 is water.
Mol Chain Residues
7
B
344
7
A
288
7
E
2
Total
13
Total
13
Atoms
C
10
C
10
Atoms
Total O
344 344
Total O
288 288
Total O
2
2
N
1
N
1
ZeroOcc AltConf
O
2
O
2
0
0
0
0
ZeroOcc AltConf
0
0
0
0
0
0
5EFN
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wwPDB X-ray Structure Validation Summary Report
3 Residue-property plots
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5EFN
i
These plots are drawn for all protein, RNA and DNA chains in the entry. The rst 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 t 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: Hdac6 protein
R798
G671
F682
H683
H684
L685
V686
L761
W611
H573
E677
V565
N523
•
E515
H516
M517
K518
P519
R520
E465
W459
SER
ASN
ALA
GLY
GLY
SER
SER
P442
•
Chain B:
• Molecule 1: Hdac6 protein
R2
G3
?4
•
•
Chain F:
• Molecule 2: histone H4 tripeptide
R2
G3
?4
•
Chain E:
R798
R788
H771
S749
N746
G714
•
• Molecule 2: histone H4 tripeptide
R708
•
K672
M673
W611
H573
V561
R520
D521
E465
•
H462
SER
ASN
ALA
GLY
GLY
SER
SER
P442
I443
•
Chain A:
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wwPDB X-ray Structure Validation Summary Report
4 Data and renement 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
Renement 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 )
5EFN
O
i
Value
P 1 21 1
55.00Å 83.91Å 86.90Å
90.00◦ 98.12◦ 90.00◦
12.34 1.80
12.34 1.80
98.9 (12.34-1.80)
98.9 (12.34-1.80)
0.14
(Not available)
2.38 (at 1.80Å)
PHENIX (phenix.rene: 1.8.3_1479)
0.162 , 0.194
0.163 , 0.193
3587 reections (5.06%)
12.0
0.432
0.45 , 59.0
< |L| > = 0.48, < L2 > = 0.31
No twinning to report.
0.95
6396
15.0
Source
Depositor
Depositor
Depositor
EDS
Depositor
EDS
Depositor
Depositor
Xtriage
Depositor
Depositor
DCC
DCC
Xtriage
Xtriage
EDS
Xtriage
Xtriage
EDS
wwPDB-VP
wwPDB-VP
The largest o-origin peak in the Patterson function is 15.29% of the height of the origin peak. No signicant pseudotranslation is detected.
Xtriage's analysis on translational NCS is as follows:
1 Intensities
estimated from amplitudes.
values of < |L| >, < L2 > for acentric reections are 0.5, 0.333 respectively for untwinned datasets,
and 0.375, 0.2 for perfectly twinned datasets.
2 Theoretical
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wwPDB X-ray Structure Validation Summary Report
5 Model quality
5.1
O
5EFN
i
Standard geometry
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Bond lengths and bond angles in the following residue types are not validated in this section: ZN,
MCM, 5OL, K, EDO
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).
Bond lengths Bond angles
Mol Chain RMSZ
#|Z| >5 RMSZ #|Z| >5
1
1
2
2
All
A
B
E
F
All
0.33
0.35
0.14
0.17
0.34
0/2924
0/2955
0/8
0/8
0/5895
0.48
0.50
0.27
0.30
0.49
0/3964
0/4007
0/9
0/9
0/7989
There are no bond length outliers.
There are no bond angle outliers.
There are no chirality outliers.
There are no planarity outliers.
5.2
Too-close contacts
O
i
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 Chain Non-H H(model) H(added) Clashes Symm-Clashes
1
1
2
2
3
3
4
4
5
A
B
E
F
A
B
A
B
A
2830
2844
22
22
1
1
2
2
4
0
0
0
0
0
0
0
0
0
2765
2790
4
4
0
0
0
0
6
11
6
1
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Continued on next page...
Page 10
wwPDB X-ray Structure Validation Summary Report
5EFN
Continued from previous page...
Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes
5
6
6
7
7
7
All
B
E
F
A
B
E
All
8
13
13
288
344
2
6396
0
0
0
0
0
0
0
12
8
8
0
0
0
5597
0
1
2
5
2
0
20
0
0
0
0
0
0
0
The all-atom clashscore is dened as the number of clashes found per 1000 atoms (including
hydrogen atoms). The all-atom clashscore for this structure is 2.
The worst 5 of 20 close contacts within the same asymmetric unit are listed below, sorted by their
clash magnitude.
Atom-1
Atom-2
1:A:788:ARG:NH1
1:A:708:ARG:NH1
1:A:520:ARG:NH1
1:A:684:HIS:NE2
1:B:671:GLY:N
7:A:905:HOH:O
7:A:901:HOH:O
1:A:521:ASP:OD1
7:A:904:HOH:O
7:B:903:HOH:O
Interatomic
distance (Å)
2.37
2.28
2.43
2.35
2.36
Clash
overlap (Å)
0.57
0.57
0.52
0.50
0.50
There are no symmetry-related clashes.
5.3
Torsion angles
O
i
5.3.1 Protein backbone O
i
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
1
A
366/364 (100%)
1
B
2
Favoured Allowed Outliers Percentiles
358 (98%)
8 (2%)
0
100
100
368/364 (101%)
359 (98%)
9 (2%)
0
100
100
E
1/3 (33%)
1 (100%)
0
0
100
100
2
F
1/3 (33%)
1 (100%)
0
0
100
100
All
All
736/734 (100%)
719 (98%)
17 (2%)
0
100
100
Page 11
wwPDB X-ray Structure Validation Summary Report
5EFN
There are no Ramachandran outliers to report.
5.3.2 Protein sidechains O
i
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
1
A
308/304 (101%)
1
B
All
All
Rotameric Outliers Percentiles
302 (98%)
6 (2%)
65
52
312/304 (103%)
308 (99%)
4 (1%)
76
68
620/608 (102%)
610 (98%)
10 (2%)
72
59
5 of 10 residues with a non-rotameric sidechain are listed below:
Mol Chain Res Type
1
1
1
1
1
A
A
A
B
A
443
465
611
611
573
ILE
GLU
TRP
TRP
HIS
Some sidechains can be ipped to improve hydrogen bonding and reduce clashes. There are no
such sidechains identied.
5.3.3 RNA O
i
There are no RNA molecules in this entry.
5.4
Non-standard residues in protein, DNA, RNA chains
O
i
2 non-standard protein/DNA/RNA residues are modelled in this entry.
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 dened 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).
Page 12
wwPDB X-ray Structure Validation Summary Report
Mol Type Chain Res Link
Bond lengths
2
5OL
E
4
3,2,6
Counts
8,12,13
2
5OL
F
4
3,2,6
8,12,13
5EFN
Bond angles
RMSZ
1.80
#|Z| > 2
2 (25%)
Counts
10,15,17
RMSZ
1.38
#|Z| > 2
2 (20%)
1.73
2 (25%)
10,15,17
1.15
1 (10%)
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 dened in the chemical
component dictionary. Similar counts are reported in the Torsion and Rings columns. '-' means
no outliers of that kind were identied.
Mol Type Chain Res Link Chirals Torsions Rings
2
2
5OL
5OL
E
F
4
4
3,2,6
3,2,6
-
0/6/11/13
0/6/11/13
0/0/0/0
0/0/0/0
All (4) bond length outliers are listed below:
Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)
2
2
2
2
E
F
F
E
4
4
4
4
5OL
5OL
5OL
5OL
O02-C08
O02-C08
O01-C08
O01-C08
2.49
2.51
3.01
3.37
1.41
1.41
1.42
1.43
1.38
1.38
1.38
1.38
All (3) bond angle outliers are listed below:
Mol Chain Res Type
2
2
2
E
E
F
4
4
4
5OL
5OL
5OL
Atoms
C06-N07-C08
O-C-CA
O-C-CA
Z Observed( ) Ideal( )
o
-3.11
-2.57
-2.56
112.86
118.83
118.85
There are no chirality outliers.
There are no torsion outliers.
There are no ring outliers.
2 monomers are involved in 2 short contacts:
Mol Chain Res Type Clashes Symm-Clashes
2
2
5.5
E
F
4
4
5OL
5OL
Carbohydrates
1
1
O
i
There are no carbohydrates in this entry.
0
0
o
116.84
125.72
125.72
Page 13
5.6
wwPDB X-ray Structure Validation Summary Report
Ligand geometry
5EFN
O
i
Of 11 ligands modelled in this entry, 6 are monoatomic - leaving 5 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 dened 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
Bond lengths
5
5
5
6
EDO
EDO
EDO
MCM
A
B
B
E
804
804
805
101
2
Counts
3,3,3
3,3,3
3,3,3
13,14,14
6
MCM
F
101
2
13,14,14
Bond angles
RMSZ
0.42
0.44
0.43
1.91
#|Z| > 2
0
0
0
2 (15%)
Counts
2,2,2
2,2,2
2,2,2
13,20,20
RMSZ
0.49
0.29
0.44
1.15
#|Z| > 2
0
0
0
2 (15%)
1.93
2 (15%)
13,20,20
1.12
1 (7%)
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 dened in the chemical
component dictionary. Similar counts are reported in the Torsion and Rings columns. '-' means
no outliers of that kind were identied.
Mol Type Chain Res Link Chirals Torsions Rings
5
5
5
6
6
EDO
EDO
EDO
MCM
MCM
A
B
B
E
F
804
804
805
101
101
2
2
-
0/1/1/1
0/1/1/1
0/1/1/1
0/0/0/0
0/0/0/0
0/0/0/0
0/0/0/0
0/0/0/0
0/2/2/2
0/2/2/2
All (4) bond length outliers are listed below:
Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)
6
6
6
6
F
E
E
F
101
101
101
101
MCM
MCM
MCM
MCM
C6-C7
C6-C7
C7-C3
C7-C3
3.23
3.24
5.27
5.46
1.49
1.49
1.48
1.48
1.42
1.42
1.41
1.41
All (3) bond angle outliers are listed below:
Mol Chain Res Type Atoms
6
E
101
MCM
C9-CA-N
Z Observed( ) Ideal( )
o
-2.10
116.57
o
120.88
Continued on next page...
Page 14
wwPDB X-ray Structure Validation Summary Report
Continued from previous page...
Mol Chain Res Type Atoms
6
6
E
F
101
101
MCM
MCM
O1-C4-C5
O1-C4-C5
Z Observed( ) Ideal( )
o
2.10
2.26
121.71
121.88
There are no chirality outliers.
There are no torsion outliers.
There are no ring outliers.
2 monomers are involved in 3 short contacts:
Mol Chain Res Type Clashes Symm-Clashes
6
6
5.7
E
F
101
101
MCM
MCM
Other polymers
1
2
0
0
O
i
There are no such residues in this entry.
5.8
Polymer linkage issues
O
There are no chain breaks in this entry.
i
o
119.39
119.39
5EFN
Page 15
wwPDB X-ray Structure Validation Summary Report
6 Fit of model and data
6.1
O
5EFN
i
Protein, DNA and RNA chains
O
i
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
1
A
357/364 (98%)
1
B
2
RSRZ>
RSRZ>2
<
OWAB(Å ) Q<0.9
2
#
-0.44
4 (1%) 82
80
7, 14, 29, 43
0
357/364 (98%)
-0.62
2 (0%) 90
88
6, 11, 22, 38
0
E
2/3 (66%)
2.75
1 (50%) 0
0
65, 65, 65, 76
0
2
F
2/3 (66%)
2.44
2 (100%) 0
0
64, 64, 64, 74
0
All
All
718/734 (97%)
-0.51
9 (1%) 79
76
6, 12, 27, 76
0
The worst 5 of 9 RSRZ outliers are listed below:
Mol Chain Res Type RSRZ
1
1
1
2
1
6.2
A
A
B
E
A
462
442
442
2
771
HIS
PRO
PRO
ARG
HIS
4.7
4.6
4.4
3.6
3.4
Non-standard residues in protein, DNA, RNA chains
O
i
In the following table, the Atoms column lists the number of modelled atoms in the group and the
number dened 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 Type Chain Res Atoms RSCC RSR LLDF B-factors(Å ) Q<0.9
2
2
2
5OL
5OL
E
F
4
4
13/14
13/14
0.87
0.87
0.14
0.15
-
18,20,23,24
16,23,28,28
0
0
Page 16
6.3
wwPDB X-ray Structure Validation Summary Report
Carbohydrates
5EFN
O
i
There are no carbohydrates in this entry.
6.4
Ligands
O
i
In the following table, the Atoms column lists the number of modelled atoms in the group and the
number dened 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 Type Chain Res Atoms RSCC RSR LLDF B-factors(Å ) Q<0.9
2
6
6
3
4
3
4
4
4
5
5
5
6.5
MCM
MCM
ZN
K
ZN
K
K
K
EDO
EDO
EDO
F
E
B
A
A
B
A
B
A
B
B
101
101
801
803
801
803
802
802
804
805
804
Other polymers
13/13
13/13
1/1
1/1
1/1
1/1
1/1
1/1
4/4
4/4
4/4
O
i
There are no such residues in this entry.
0.84
0.82
1.00
0.99
1.00
1.00
1.00
1.00
0.89
0.85
0.83
0.20
0.17
0.04
0.04
0.04
0.02
0.03
0.02
0.15
0.25
0.29
2.00
0.59
-1.93
-2.74
-2.89
-3.58
-3.80
-4.60
-
30,35,40,42
25,31,36,38
16,16,16,16
12,12,12,12
18,18,18,18
9,9,9,9
10,10,10,10
9,9,9,9
31,31,32,32
34,35,35,35
16,18,19,20
0
0
1
0
1
0
0
0
4
4
4