- PDB-2ox7: Crystal structure of protein EF1440 from Enterococcus faecalis -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2ox7
Title
Crystal structure of protein EF1440 from Enterococcus faecalis
Components
Hypothetical protein
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / HYPOTHETICAL PROTEIN / PSI / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM / NYSGRC / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information
YopX-like domains / YopX-like domains / Conserved hypothetical protein CHP1671 / YopX-like, C-terminal / YopX protein / YopX protein / SH3 type barrels. / Roll / Mainly Beta Similarity search - Domain/homology
Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 18, 2007 / Details: SGX-CAT
Radiation
Monochromator: SGX-CAT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97961 Å / Relative weight: 1
Reflection
Redundancy: 14.4 % / Av σ(I) over netI: 6.2 / Number: 957551 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / D res high: 1.777 Å / D res low: 25.474 Å / Num. obs: 66447 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Rsym value
Redundancy
5.62
25.47
98.5
1
0.055
0.055
13.1
3.97
5.62
100
1
0.056
0.056
14.4
3.25
3.97
100
1
0.058
0.058
14.7
2.81
3.25
100
1
0.072
0.072
14.8
2.51
2.81
100
1
0.09
0.09
14.8
2.29
2.51
100
1
0.109
0.109
14.8
2.12
2.29
100
1
0.117
0.117
14.8
1.99
2.12
100
1
0.158
0.158
14.8
1.87
1.99
100
1
0.253
0.253
14.8
1.78
1.87
96.1
1
0.383
0.383
12.6
Reflection
Resolution: 1.777→25.474 Å / Num. obs: 66447 / % possible obs: 99.4 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 6.2
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.777-1.87
12.6
0.383
2
116843
9276
0.383
96.1
1.87-1.99
14.8
0.253
3
134736
9114
0.253
100
1.99-2.12
14.8
0.158
4.7
127570
8608
0.158
100
2.12-2.29
14.8
0.117
6.2
118862
8013
0.117
100
2.29-2.51
14.8
0.109
6.3
109642
7395
0.109
100
2.51-2.81
14.8
0.09
7.3
99844
6733
0.09
100
2.81-3.25
14.8
0.072
8.8
87635
5927
0.072
100
3.25-3.97
14.7
0.058
10.5
75018
5113
0.058
100
3.97-5.62
14.4
0.056
10.4
57330
3973
0.056
100
5.62-25.47
13.1
0.055
11.2
30071
2295
0.055
98.5
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Phasing
Phasing
Method: SAD
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Processing
Software
Name
Version
Classification
NB
SCALA
datascaling
SHELX
phasing
REFMAC
refinement
PDB_EXTRACT
2
dataextraction
MAR345
CCD
datacollection
MOSFLM
datareduction
CCP4
(SCALA)
datascaling
SHELXD
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.777→19.63 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.532 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23531
3366
5.1 %
RANDOM
Rwork
0.18973
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-
obs
0.19208
62920
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 33.085 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0 Å2
0 Å2
0 Å2
2-
-
0 Å2
0 Å2
3-
-
-
0 Å2
Refinement step
Cycle: LAST / Resolution: 1.777→19.63 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4714
0
0
663
5377
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
4842
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.532
1.945
6564
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.622
5
570
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.686
24.646
254
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.014
15
808
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.788
15
20
X-RAY DIFFRACTION
r_chiral_restr
0.115
0.2
690
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
3756
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.209
0.2
2200
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.32
0.2
3353
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.174
0.2
540
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.209
0.2
122
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.164
0.2
54
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.465
1.5
2946
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.086
2
4628
X-RAY DIFFRACTION
r_scbond_it
3.105
3
2215
X-RAY DIFFRACTION
r_scangle_it
4.319
4.5
1936
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.777→1.826 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.279
210
-
Rwork
0.212
4466
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obs
-
-
97.44 %
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