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Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant S. aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LKF PDB entry 1LKF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 10 mg/mL protein in 10 mM fos-choline 14, 30 mM beta-OG, 10 mM sodium acetate, pH 5.4 against reservoir solution of 28% PEG400, 0.2 M magnesium chloride, 0.1 M HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.82 56.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.202 α = 90 b = 37.769 β = 119.8 c = 77.914 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment 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 2016-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.977 CHESS F1
Data Collection Overall 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 1.5 67.61 97.8 0.054 0.989 9.7 3.2 59415
Highest Resolution Shell 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 1.5 1.53 84.7 0.27 0.961 4.4 3
Refinement Statistics 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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1LKF 1.5 67.61 56377 3038 97.72 0.1636 0.1623 0.1733 0.1883 0.1957 RANDOM 29.138
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] -0.08 -0.37 3.56 -1.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.914 r_dihedral_angle_4_deg 14.277 r_dihedral_angle_3_deg 11.324 r_dihedral_angle_1_deg 6.806 r_angle_refined_deg 1.884 r_angle_other_deg 0.992 r_chiral_restr 0.126 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.914 r_dihedral_angle_4_deg 14.277 r_dihedral_angle_3_deg 11.324 r_dihedral_angle_1_deg 6.806 r_angle_refined_deg 1.884 r_angle_other_deg 0.992 r_chiral_restr 0.126 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2386 Nucleic Acid Atoms Solvent Atoms 433 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing