3HO7
Crystal structure of OxyR from Porphyromonas gingivalis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 291.15 | 12% PEG 8K, 8% EG, 0.1M HEPES BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K |
2 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 291.15 | 12% PEG 8K, 8% EG, 0.1M HEPES BUFFER, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.819 | α = 110.63 |
b = 55.795 | β = 102.82 |
c = 56.711 | γ = 114.63 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 93 | IMAGE PLATE | RIGAKU RAXIS IV++ | MSC Varimax confocal optics | 2009-02-04 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 93 | IMAGE PLATE | RIGAKU RAXIS IV++ | MSC Varimax confocal optics | 2009-03-19 | M | SINGLE WAVELENGTH | |||||
3 | 1 | x-ray | 93 | IMAGE PLATE | RIGAKU RAXIS IV++ | MSC Varimax confocal optics | 2009-03-27 | M | SINGLE WAVELENGTH | |||||
1,2,3 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.5418 | ||
2 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.5418 | ||
3 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | ||||||||
1,2,3 | 1.58 | 26.94 | 86.2 | 0.032 | 3.92 | 127008 | 59646 | 3 | 3.7 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
1,2,3 | 1.58 | 86.2 | 0.032 | 3.92 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | 1.58 | 26.94 | 59646 | 57380 | 2033 | 83.56 | 0.22028 | 0.2194 | 0.24456 | RANDOM | 33.429 |
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] | |
1.25 | 0.59 | -6.77 | 1.22 | 5.57 | -2.47 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.562 |
r_dihedral_angle_3_deg | 11.367 |
r_dihedral_angle_4_deg | 10.566 |
r_dihedral_angle_1_deg | 4.283 |
r_scangle_it | 0.856 |
r_angle_refined_deg | 0.648 |
r_scbond_it | 0.538 |
r_mcangle_it | 0.385 |
r_mcbond_it | 0.21 |
r_chiral_restr | 0.043 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3534 |
Nucleic Acid Atoms | |
Solvent Atoms | 418 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
CrystalClear | data collection |
PHENIX | model building |
REFMAC | refinement |
d*TREK | data reduction |
CrystalClear | data scaling |
PHENIX | phasing |