- PDB-3gy0: Crystal structure of putatitve short chain dehydrogenase FROM SHI... -
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Basic information
Entry
Database: PDB / ID: 3gy0
Title
Crystal structure of putatitve short chain dehydrogenase FROM SHIGELLA FLEXNERI 2A STR. 301 complexed with NADP
Components
dehydrogenase
Keywords
OXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGXRC / short chain dehydrogenase / NADP / 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: 5.1 % / Av σ(I) over netI: 28.62 / Number: 495769 / Rmerge(I) obs: 0.069 / Χ2: 1.48 / D res high: 1.55 Å / D res low: 50 Å / Num. obs: 96819 / % possible obs: 94
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
4.21
50
98.8
1
0.035
2.413
5.7
3.34
4.21
100
1
0.039
2.375
5.5
2.92
3.34
100
1
0.055
2.449
5.6
2.65
2.92
100
1
0.064
2.048
5.7
2.46
2.65
100
1
0.071
1.654
5.7
2.32
2.46
100
1
0.086
1.549
5.7
2.2
2.32
100
1
0.105
1.454
5.7
2.1
2.2
100
1
0.128
1.382
5.7
2.02
2.1
100
1
0.167
1.308
5.7
1.95
2.02
100
1
0.224
1.202
5.7
1.89
1.95
100
1
0.283
1.149
5.7
1.84
1.89
100
1
0.376
1.097
5.7
1.79
1.84
100
1
0.467
1.038
5.6
1.75
1.79
100
1
0.555
1.024
5.5
1.71
1.75
100
1
0.677
1.019
5.1
1.67
1.71
99.6
1
0.742
0.95
4.4
1.64
1.67
95.4
1
0.829
0.973
3.6
1.61
1.64
85
1
0.921
0.92
2.9
1.58
1.61
62.4
1
0.982
0.833
2.1
1.55
1.58
39.2
1
0.883
1.7
Reflection
Resolution: 1.55→50 Å / Num. obs: 96819 / % possible obs: 94 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.069 / Χ2: 1.482 / Net I/σ(I): 28.615
Reflection shell
Resolution (Å)
Redundancy (%)
Num. unique all
Χ2
Diffraction-ID
% possible all
Rmerge(I) obs
1.55-1.58
1.7
2024
0.883
1
39.2
1.58-1.61
2.1
3187
0.833
1
62.4
0.982
1.61-1.64
2.9
4426
0.92
1
85
0.921
1.64-1.67
3.6
4867
0.973
1
95.4
0.829
1.67-1.71
4.4
5144
0.95
1
99.6
0.742
1.71-1.75
5.1
5126
1.019
1
100
0.677
1.75-1.79
5.5
5202
1.024
1
100
0.555
1.79-1.84
5.6
5142
1.038
1
100
0.467
1.84-1.89
5.7
5104
1.097
1
100
0.376
1.89-1.95
5.7
5146
1.149
1
100
0.283
1.95-2.02
5.7
5168
1.202
1
100
0.224
2.02-2.1
5.7
5148
1.308
1
100
0.167
2.1-2.2
5.7
5102
1.382
1
100
0.128
2.2-2.32
5.7
5191
1.454
1
100
0.105
2.32-2.46
5.7
5122
1.549
1
100
0.086
2.46-2.65
5.7
5158
1.654
1
100
0.071
2.65-2.92
5.7
5152
2.048
1
100
0.064
2.92-3.34
5.6
5168
2.449
1
100
0.055
3.34-4.21
5.5
5135
2.375
1
100
0.039
4.21-50
5.7
5107
2.413
1
98.8
0.035
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Phasing
Phasing
Method: molecular replacement
Phasing MR
Rfactor: 38.66 / Model details: Phaser MODE: MR_AUTO
Highest resolution
Lowest resolution
Rotation
3.5 Å
38.89 Å
Translation
3.5 Å
38.89 Å
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
PHASER
phasing
REFMAC
refinement
PDB_EXTRACT
3.006
dataextraction
CBASS
datacollection
HKL-2000
datareduction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.181 / WRfactor Rwork: 0.16 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.899 / SU B: 2.628 / SU ML: 0.041 / SU R Cruickshank DPI: 0.064 / SU Rfree: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.193
2595
5.1 %
RANDOM
Rwork
0.17
-
-
-
obs
0.171
51188
95.76 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
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