6U4P
Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant S. aureus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.2 | 298 | 10 mg/mL protein in 10 mM sodium acetate, pH 5.4, 25 mM Fos-Choline-14, 40 mM beta-OG against reservoir solution of 1.9 M ammonium sulfate, 0.25 M potassium sodium tartrate, 0.1 M sodium citrate, pH 5.2 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.86 | 56.96 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 151.174 | α = 90 |
b = 134.616 | β = 91.84 |
c = 130.697 | 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 | PIXEL | DECTRIS PILATUS 6M | 2018-11-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.979 | SSRL | BL9-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 2.49 | 37.8 | 96.5 | 0.061 | 0.968 | 10.2 | 3.4 | 87452 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.49 | 2.56 | 98.1 | 0.515 | 0.864 | 2.4 | 3.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | PDB entry 6U49 | 2.49 | 37.8 | 83195 | 4257 | 96.2 | 0.2139 | 0.2121 | 0.2495 | RANDOM | 75.524 |
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] | |
-0.6 | 0.65 | -1.97 | 2.53 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.817 |
r_dihedral_angle_3_deg | 19.908 |
r_dihedral_angle_4_deg | 16.946 |
r_dihedral_angle_1_deg | 7.212 |
r_angle_refined_deg | 1.988 |
r_chiral_restr | 0.144 |
r_bond_refined_d | 0.011 |
r_gen_planes_refined | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 16380 |
Nucleic Acid Atoms | |
Solvent Atoms | 114 |
Heterogen Atoms | 320 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |