3DJB
Crystal structure of a HD-superfamily hydrolase (BT9727_1981) from Bacillus thuringiensis, Northeast Structural Genomics Consortium Target BuR114
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | microbatch under oil | 7.5 | 291 | Protein solution: 10 mM Tris (pH 7.5), 100 mM NaCl, and 5 mM DTT. Reservoir solution: 100 mM Hepes (pH 7.5), 40% PEG 1k, and 100 mM KNO3., microbatch under oil, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.11 | 41.82 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 66.273 | α = 90 |
b = 66.273 | β = 90 |
c = 101.736 | γ = 90 |
Symmetry | |
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Space Group | P 43 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 4 | mirrors | 2007-01-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4A | 0.97907 | NSLS | X4A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||||
1 | 2.9 | 30 | 98.2 | 0.069 | 0.056 | 24.3 | 4.9 | 19157 | 18813 | 65.2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.9 | 3 | 100 | 0.42 | 0.351 | 2.5 | 4.8 | 1939 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.9 | 19.45 | 2 | 2 | 19078 | 15854 | 1493 | 83.1 | 0.247 | 0.246 | 0.246 | 0.291 | RANDOM | 71.2 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.58 | 0.58 | -1.16 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 20.7 |
c_angle_deg | 1.1 |
c_improper_angle_d | 0.7 |
c_bond_d | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3046 |
Nucleic Acid Atoms | |
Solvent Atoms | 12 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
ADSC | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
SHELX | phasing |