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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 1PVL PDB entry 1PVL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 10 mg/mL protein in 10 mM sodium acetate, pH 5.4, 10 mM Fos-Choline 14, 30 mM beta-OG against reservoir solution of 2.6 M ammonium sulfate, 5% PEG400, 0.1 M HEPES, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.76 55.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.249 α = 90 b = 49.249 β = 90 c = 266.867 γ = 120
Symmetry Space Group P 32 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 2018-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979 SSRL BL9-2
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 1.78 89 99.7 0.035 0.999 18.9 9.4 37358
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 1.78 1.82 98.2 0.109 0.997 20 9.2
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 1PVL 1.78 38.49 35471 1887 99.75 0.1792 0.1776 0.1793 0.2099 0.2112 RANDOM 29.861
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] 0.67 0.33 0.67 -2.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.013 r_dihedral_angle_3_deg 16.027 r_dihedral_angle_4_deg 10.5 r_dihedral_angle_1_deg 6.964 r_angle_refined_deg 2.438 r_chiral_restr 0.203 r_bond_refined_d 0.017 r_gen_planes_refined 0.017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2389 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing