3U2K
S. aureus GyrB ATPase domain in complex with a small molecule inhibitor
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | sitting drop, inhibitor soak | 7.5 | 293 | 19-30% PEG3350, 0.1MHepes, pH 7.5, 0.2M MgCl2, sitting drop, inhibitor soak, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.67 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 143.175 | α = 90 |
b = 55.497 | β = 100.67 |
c = 51.349 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | RIGAKU SATURN 944 | mirrors | 2010-11-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
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 | 1.64 | 35.175 | 88.3 | 0.024 | 21.8 | 2.7 | 124850 | 43084 | 1 | 1 |
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) | ||||||||||
1 | 1.64 | 1.73 | 72.6 | 0.18 | 0.18 | 4.4 | 1.9 | 5136 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1.64 | 35.17 | 42877 | 2181 | 88.15 | 0.1575 | 0.1562 | 0.182 | RANDOM | 16.4114 |
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] | |
-0.13 | -0.19 | 0.11 | -0.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.629 |
r_dihedral_angle_4_deg | 15.928 |
r_dihedral_angle_3_deg | 12.12 |
r_dihedral_angle_1_deg | 5.265 |
r_scangle_it | 3.237 |
r_scbond_it | 1.869 |
r_angle_refined_deg | 1.062 |
r_mcangle_it | 0.968 |
r_angle_other_deg | 0.769 |
r_mcbond_it | 0.485 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3058 |
Nucleic Acid Atoms | |
Solvent Atoms | 440 |
Heterogen Atoms | 60 |
Software
Software | |
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Software Name | Purpose |
d*TREK | data scaling |
SCALA | data scaling |
AMoRE | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
JDirector | data collection |
XDS | data reduction |