- PDB-3gms: Crystal structure of putative NADPH:quinone reductase from bacill... -
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Basic information
Entry
Database: PDB / ID: 3gms
Title
Crystal structure of putative NADPH:quinone reductase from bacillus thuringiensis
Components
Putative NADPH:quinone reductase
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / putative quinone oxidoreductase / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Resolution: 1.76→50 Å / Num. obs: 76483 / % possible obs: 98.3 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.069 / Χ2: 1.291 / Net I/σ(I): 17.826
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
% possible all
1.76-1.82
2.8
0.367
7462
0.76
95.5
1.82-1.9
3
0.29
7730
0.822
99.5
1.9-1.98
3.1
0.23
7736
0.97
99.9
1.98-2.09
3.2
0.159
7789
1.129
99.8
2.09-2.22
3.2
0.114
7718
1.288
99.8
2.22-2.39
3.2
0.094
7746
1.553
99.8
2.39-2.63
3.2
0.075
7800
1.531
99.8
2.63-3.01
3.2
0.063
7734
1.624
99.7
3.01-3.79
3
0.056
7530
1.741
96.5
3.79-50
2.9
0.051
7238
1.414
93.1
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
REFMAC
refinement
PDB_EXTRACT
3.006
dataextraction
CBASS
datacollection
HKL-2000
datareduction
SHELXD
phasing
SHELXE
modelbuilding
CCP4
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.76→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.242 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.842 / SU B: 2.488 / SU ML: 0.079 / SU R Cruickshank DPI: 0.117 / SU Rfree: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY. 3. The Friedel pairs were used in phasing.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.234
1955
5 %
RANDOM
Rwork
0.199
-
-
-
obs
0.2
38977
98.56 %
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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: MASK
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