3HJG
Crystal structure of putative alpha-ribazole-5'-phosphate phosphatase CobC FROM Vibrio parahaemolyticus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 294 | 5% ISOPROPANOL, 2000 MM AMMONIUM SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, pH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
6.2 | 80.17 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 107.215 | α = 90 |
b = 107.215 | β = 90 |
c = 206.717 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 | 90 | CCD | ADSC QUANTUM 315 | MIRRORS | 2009-04-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | NSLS | X29A |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.61 | 50 | 99.9 | 0.132 | 5 | 6.5 | 37362 | -0.5 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.61 | 2.7 | 99.6 | 0.94 | 0.8 | 5 |
Refinement
Statistics | |||||||||||||||||||
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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 | SAD | THROUGHOUT | 2.8 | 20 | 26642 | 849 | 90.51 | 0.26331 | 0.26275 | 0.28009 | RANDOM | 127.928 |
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] | |
-4.25 | -4.25 | 8.5 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.26 |
r_dihedral_angle_3_deg | 20.321 |
r_dihedral_angle_4_deg | 16.03 |
r_dihedral_angle_1_deg | 6.92 |
r_scangle_it | 6.262 |
r_scbond_it | 3.932 |
r_mcangle_it | 3.504 |
r_mcbond_it | 1.895 |
r_angle_refined_deg | 1.153 |
r_nbtor_refined | 0.298 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3194 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
SHELXD | phasing |
REFMAC | refinement |
DENZO | data reduction |
HKL-2000 | data scaling |