- PDB-3g1t: CRYSTAL STRUCTURE OF short chain dehydrogenase from Salmonella en... -
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Basic information
Entry
Database: PDB / ID: 3g1t
Title
CRYSTAL STRUCTURE OF short chain dehydrogenase from Salmonella enterica subsp. enterica serovar Typhi str. CT18
Components
short chain dehydrogenase
Keywords
OXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / short chain dehydrogenase / 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: 20.1 % / Av σ(I) over netI: 45 / Number: 1102293 / Rmerge(I) obs: 0.133 / Χ2: 2.75 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 54881 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
4.61
50
99.3
1
0.063
3.603
21.7
3.66
4.61
99.5
1
0.095
6.07
19.5
3.2
3.66
99.6
1
0.115
6.055
20.3
2.91
3.2
100
1
0.138
5.396
21.9
2.7
2.91
100
1
0.152
4.81
22
2.54
2.7
100
1
0.169
3.94
22
2.41
2.54
100
1
0.183
3.512
22.1
2.31
2.41
100
1
0.198
2.963
22.1
2.22
2.31
100
1
0.212
2.486
22
2.14
2.22
100
1
0.234
2.206
22.1
2.07
2.14
100
1
0.262
1.91
22.1
2.02
2.07
100
1
0.291
1.65
22.1
1.96
2.02
100
1
0.326
1.423
22.1
1.91
1.96
100
1
0.374
1.159
22
1.87
1.91
100
1
0.471
1.038
21.7
1.83
1.87
100
1
0.535
0.925
20.9
1.79
1.83
100
1
0.565
0.893
18.8
1.76
1.79
100
1
0.59
0.838
14.9
1.73
1.76
99.5
1
0.634
0.824
11.8
1.7
1.73
93.5
1
0.642
0.791
9.2
Reflection
Resolution: 1.7→50 Å / Num. obs: 54881 / % possible obs: 99.6 % / Redundancy: 20.1 % / Rmerge(I) obs: 0.133 / Χ2: 2.751 / Net I/σ(I): 45
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
Diffraction-ID
% possible all
1.7-1.73
9.2
0.642
2670
0.791
1
93.5
1.73-1.76
11.8
0.634
2652
0.824
1
99.5
1.76-1.79
14.9
0.59
2800
0.838
1
100
1.79-1.83
18.8
0.565
2703
0.893
1
100
1.83-1.87
20.9
0.535
2766
0.925
1
100
1.87-1.91
21.7
0.471
2746
1.038
1
100
1.91-1.96
22
0.374
2731
1.159
1
100
1.96-2.02
22.1
0.326
2791
1.423
1
100
2.02-2.07
22.1
0.291
2710
1.65
1
100
2.07-2.14
22.1
0.262
2739
1.91
1
100
2.14-2.22
22.1
0.234
2780
2.206
1
100
2.22-2.31
22
0.212
2768
2.486
1
100
2.31-2.41
22.1
0.198
2739
2.963
1
100
2.41-2.54
22.1
0.183
2769
3.512
1
100
2.54-2.7
22
0.169
2750
3.94
1
100
2.7-2.91
22
0.152
2726
4.81
1
100
2.91-3.2
21.9
0.138
2769
5.396
1
100
3.2-3.66
20.3
0.115
2727
6.055
1
99.6
3.66-4.61
19.5
0.095
2739
6.07
1
99.5
4.61-50
21.7
0.063
2806
3.603
1
99.3
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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
CBASS
datacollection
HKL-2000
datareduction
SHELXD
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.172 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.864 / SU B: 5.095 / SU ML: 0.076 / SU R Cruickshank DPI: 0.106 / SU Rfree: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.111 / 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
0.232
1532
5 %
RANDOM
Rwork
0.185
-
-
-
obs
0.188
30391
98.44 %
-
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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