2HQ5
Crystal structure of multidrug binding protein QacR from Staphylococcus aureus cocrystallized with compound DB359
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1JT6 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 298 | Between 2.3 and 2.7M Ammonium Sulfate in 0.1M Sodium Acetate, Protein was set up at 10mg/mL with a ligand concentration between 200 and 500 micromolar, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.77 | 67.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 171.366 | α = 90 |
b = 171.366 | β = 90 |
c = 94.496 | γ = 90 |
Symmetry | |
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Space Group | P 42 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 | 100 | CCD | ADSC QUANTUM 210 | 2004-12-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.1 | 1.0 | ALS | 8.2.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.8 | 63.48 | 96.2 | 0.052 | 0.052 | 5.1 | 35246 | 33907 |
Highest Resolution Shell | |||||||||||||||||||
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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) | ||||||||||
2.8 | 2.95 | 88.4 | 0.412 | 0.412 | 3.1 | 3.6 | 4432 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1jt6 | 2.8 | 63.48 | 35246 | 33907 | 3384 | 96.2 | 0.213 | 0.213 | 0.259 | RANDOM | 71.2 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
4.6 | 4.6 | -9.21 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 18.2 |
c_angle_deg | 1.2 |
c_improper_angle_d | 0.7 |
c_bond_d | 0.007 |
c_bond_d_na | |
c_bond_d_prot | |
c_angle_d | |
c_angle_d_na | |
c_angle_d_prot | |
c_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6133 |
Nucleic Acid Atoms | |
Solvent Atoms | 37 |
Heterogen Atoms | 70 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |