1VPM
Crystal structure of Acyl-CoA hydrolase (NP_241664.1) from Bacillus halodurans at 1.66 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 293 | 0.15M Na formate, 20.00% PEG 3350, 0.033M Cl2E9, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 48.39 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 82.984 | α = 90 |
b = 106.507 | β = 90 |
c = 120.254 | γ = 90 |
Symmetry | |
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Space Group | I 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC | 2004-10-09 | M | MAD | ||||||
2 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 0.979764,1.019943,0.979648 | ALS | 8.3.1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.66 | 28.75 | 99.5 | 0.099 | 13 | 5.9 | 62701 | 33.53 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.66 | 1.75 | 98.5 | 0.553 | 2.8 | 3.5 | 8969 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MAD | THROUGHOUT | 1.66 | 28.75 | 59512 | 3188 | 99.36 | 0.17146 | 0.17012 | 0.19669 | RANDOM | 26.825 |
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] | |
2.4 | -0.37 | -2.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.085 |
r_dihedral_angle_4_deg | 18.924 |
r_dihedral_angle_3_deg | 12.879 |
r_scangle_it | 7.504 |
r_dihedral_angle_1_deg | 6.613 |
r_scbond_it | 5.79 |
r_mcangle_it | 3.274 |
r_mcbond_it | 2.635 |
r_angle_refined_deg | 1.728 |
r_angle_other_deg | 0.887 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3481 |
Nucleic Acid Atoms | |
Solvent Atoms | 310 |
Heterogen Atoms | 101 |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
SCALA | data scaling |
SHELX | model building |
REFMAC | refinement |
XDS | data reduction |
CCP4 | data scaling |
SHELX | phasing |
SHARP | phasing |
autoSHARP | phasing |