- PDB-3evn: CRYSTAL STRUCTURE OF putative oxidoreductase from Streptococcus a... -
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Basic information
Entry
Database: PDB / ID: 3evn
Title
CRYSTAL STRUCTURE OF putative oxidoreductase from Streptococcus agalactiae 2603V/r
Components
Oxidoreductase, Gfo/Idh/MocA family
Keywords
OXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / PSI-2 / New York SGX Research Center for Structural Genomics
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9791 Å / Relative weight: 1
Reflection
Redundancy: 7.1 % / Av σ(I) over netI: 35.36 / Number: 270038 / Rmerge(I) obs: 0.063 / Χ2: 1.39 / D res high: 1.99 Å / D res low: 50 Å / Num. obs: 37904 / % possible obs: 79.7
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
4.29
50
98.7
1
0.035
2.247
7.7
3.4
4.29
99.9
1
0.057
2.383
8
2.97
3.4
100
1
0.07
1.256
8.1
2.7
2.97
100
1
0.133
1.022
8.1
2.51
2.7
100
1
0.213
0.961
7.9
2.36
2.51
95.4
1
0.288
0.938
6.2
2.24
2.36
73.2
1
0.318
0.93
5.6
2.14
2.24
53.6
1
0.354
0.979
5.6
2.06
2.14
42.1
1
0.352
0.957
5.4
1.99
2.06
34.3
1
0.388
1.018
5.3
Reflection
Resolution: 1.99→50 Å / Num. obs: 37904 / % possible obs: 79.7 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.063 / Χ2: 1.389 / Net I/σ(I): 35.361
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
Diffraction-ID
% possible all
1.99-2.06
5.3
0.388
1623
1.018
1
34.3
2.06-2.14
5.4
0.352
2000
0.957
1
42.1
2.14-2.24
5.6
0.354
2566
0.979
1
53.6
2.24-2.36
5.6
0.318
3448
0.93
1
73.2
2.36-2.51
6.2
0.288
4560
0.938
1
95.4
2.51-2.7
7.9
0.213
4731
0.961
1
100
2.7-2.97
8.1
0.133
4765
1.022
1
100
2.97-3.4
8.1
0.07
4725
1.256
1
100
3.4-4.29
8
0.057
4747
2.383
1
99.9
4.29-50
7.7
0.035
4739
2.247
1
98.7
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Phasing
Phasing
Method: SAD
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
SHELX
phasing
REFMAC
refinement
PDB_EXTRACT
3.006
dataextraction
SHELXD
phasing
Refinement
Method to determine structure: SAD / Resolution: 2→19.54 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.27 / WRfactor Rwork: 0.2 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.788 / SU B: 9.654 / SU ML: 0.139 / SU R Cruickshank DPI: 0.272 / SU Rfree: 0.242 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.267 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.285
1011
5.2 %
RANDOM
Rwork
0.205
-
-
-
obs
0.209
19614
75.26 %
-
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
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