3I07
Crystal structure of a putative organic hydroperoxide resistance protein from Vibrio cholerae O1 biovar eltor str. N16961
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3EER | PDB ENTRY 3EER |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 291 | 0.05 Cesium chloride 0.1 M MES 30% Jeffamine M-600, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.88 | 34.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 38.026 | α = 90 |
b = 76.154 | β = 90 |
c = 79.69 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 315r | mirrors | 2008-12-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.9794 | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.5 | 20 | 94.5 | 0.04 | 27 | 4 | 37820 | 35847 | 2 | 2 | 23.8 |
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) | |||||||||||
1 | 1.5 | 1.53 | 52.4 | 0.29 | 1.9 | 1.6 | 995 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MIR | THROUGHOUT | PDB ENTRY 3EER | 1.5 | 20 | 1.9 | 1.9 | 35796 | 34011 | 1785 | 95.11 | 0.16626 | 0.16531 | 0.18454 | RANDOM | 7.34 |
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] | |
1.07 | -0.95 | -0.11 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.642 |
r_dihedral_angle_4_deg | 18.466 |
r_dihedral_angle_3_deg | 13.046 |
r_dihedral_angle_1_deg | 5.864 |
r_scangle_it | 3.221 |
r_scbond_it | 2.071 |
r_angle_refined_deg | 1.425 |
r_mcangle_it | 1.219 |
r_angle_other_deg | 0.917 |
r_mcbond_it | 0.728 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2118 |
Nucleic Acid Atoms | |
Solvent Atoms | 275 |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
SBC-Collect | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |