- PDB-3gy1: CRYSTAL STRUCTURE OF putative mandelate racemase/muconate lactoni... -
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Basic information
Entry
Database: PDB / ID: 3gy1
Title
CRYSTAL STRUCTURE OF putative mandelate racemase/muconate lactonizing protein from Clostridium beijerinckii NCIMB 8052
Components
Mandelate racemase/muconate lactonizing protein
Keywords
ISOMERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / mandelate racemase/muconate lactonizing protein / Clostridium beijerinckii NCIMB 8052 / NYSGXRC / enolase / 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: 4.8 % / Av σ(I) over netI: 12.6 / Number: 963447 / Rmerge(I) obs: 0.138 / Χ2: 1.78 / D res high: 1.56 Å / D res low: 50 Å / Num. obs: 201304 / % possible obs: 83.2
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
4.23
50
99.5
1
0.056
2.703
5.8
3.36
4.23
100
1
0.075
3.257
5.7
2.94
3.36
100
1
0.099
2.811
5.6
2.67
2.94
100
1
0.12
2.051
5.5
2.48
2.67
100
1
0.151
1.828
5.5
2.33
2.48
100
1
0.181
1.647
5.5
2.21
2.33
100
1
0.213
1.609
5.5
2.12
2.21
100
1
0.257
1.528
5.5
2.04
2.12
100
1
0.314
1.423
5.5
1.97
2.04
100
1
0.404
1.233
5.5
1.9
1.97
100
1
0.47
1.177
5.4
1.85
1.9
99.8
1
0.53
1.185
4.9
1.8
1.85
96.8
1
0.548
1.169
4.3
1.76
1.8
84.4
1
0.578
1.126
3.5
1.72
1.76
73.1
1
0.58
1.103
2.9
1.68
1.72
63.1
1
0.612
1.13
2.4
1.65
1.68
52.6
1
0.639
1.099
2.1
1.62
1.65
42.4
1
0.647
1.034
2
1.59
1.62
31.8
1
0.643
1.106
1.8
1.56
1.59
21.3
1
0.757
0.981
1.6
Reflection
Resolution: 1.56→50 Å / Num. obs: 201304 / % possible obs: 83.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.138 / Χ2: 1.781 / Net I/σ(I): 12.601
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
Diffraction-ID
% possible all
1.56-1.59
1.6
0.757
2583
0.981
1
21.3
1.59-1.62
1.8
0.643
3829
1.106
1
31.8
1.62-1.65
2
0.647
5120
1.034
1
42.4
1.65-1.68
2.1
0.639
6375
1.099
1
52.6
1.68-1.72
2.4
0.612
7655
1.13
1
63.1
1.72-1.76
2.9
0.58
8805
1.103
1
73.1
1.76-1.8
3.5
0.578
10233
1.126
1
84.4
1.8-1.85
4.3
0.548
11665
1.169
1
96.8
1.85-1.9
4.9
0.53
12051
1.185
1
99.8
1.9-1.97
5.4
0.47
12083
1.177
1
100
1.97-2.04
5.5
0.404
12131
1.233
1
100
2.04-2.12
5.5
0.314
12090
1.423
1
100
2.12-2.21
5.5
0.257
12073
1.528
1
100
2.21-2.33
5.5
0.213
12114
1.609
1
100
2.33-2.48
5.5
0.181
12060
1.647
1
100
2.48-2.67
5.5
0.151
12088
1.828
1
100
2.67-2.94
5.5
0.12
12092
2.051
1
100
2.94-3.36
5.6
0.099
12109
2.811
1
100
3.36-4.23
5.7
0.075
12063
3.257
1
100
4.23-50
5.8
0.056
12085
2.703
1
99.5
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Phasing
Phasing
Method: molecular replacement
Phasing MR
Rfactor: 52.31 / Model details: Phaser MODE: MR_AUTO
Highest resolution
Lowest resolution
Rotation
3.5 Å
46.95 Å
Translation
3.5 Å
46.95 Å
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
PHASER
phasing
REFMAC
5.5.0070
refinement
PDB_EXTRACT
3.006
dataextraction
CBASS
datacollection
HKL-2000
datareduction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→19.89 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 4.249 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.092 / 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
0.212
5347
5.1 %
RANDOM
Rwork
0.179
-
-
-
obs
0.181
105785
90.45 %
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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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