- PDB-3gor: Crystal structure of putative metal-dependent hydrolase APC36150 -
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Basic information
Entry
Database: PDB / ID: 3gor
Title
Crystal structure of putative metal-dependent hydrolase APC36150
Components
Putative metal-dependent hydrolase
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / DinB Superfamily / PSI-2 / Protein Structure Initiative / Integrated Center for Structure and Function Innovation / ISFI
Function / homology
DNA damage-inducible protein DinB / DinB family / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / NICKEL (II) ION / Putative metal-dependent hydrolase
Function and homology information
Biological species
Geobacillus stearothermophilus (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.511 Å
Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 11, 2006
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97928 Å / Relative weight: 1
Reflection
Resolution: 2.5→40 Å / Num. obs: 36943 / % possible obs: 94.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.088 / Χ2: 3.112 / Net I/σ(I): 31.776
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
% possible all
2.5-2.59
5.4
0.289
1631
1.212
78.1
2.59-2.69
5.9
0.278
1727
1.305
82.9
2.69-2.82
6.2
0.233
1826
1.494
87.7
2.82-2.96
6.5
0.214
1980
1.523
93.9
2.96-3.15
7
0.182
2069
1.703
99.2
3.15-3.39
7.3
0.125
2112
2.103
100
3.39-3.73
7.3
0.096
2107
2.765
100
3.73-4.27
7.3
0.075
2137
3.366
100
4.27-5.38
7.2
0.065
2155
4.498
100
5.38-40
6.8
0.067
2260
8.852
99.1
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
SHELX
phasing
PHENIX
refinement
PDB_EXTRACT
3.006
dataextraction
HKL-2000
datacollection
HKL-2000
datareduction
HKL-2000
datascaling
SOLVE
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.511→35.623 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The Friedel pairs were used in phasing.
Rfactor
Num. reflection
% reflection
Rfree
0.247
1887
5.11 %
Rwork
0.186
-
-
obs
0.189
36943
92.69 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.915 Å2 / ksol: 0.342 e/Å3
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