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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 7AHL PDB entry 7AHL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 8 mg/mL protein in 10 mM sodium acetate, pH 5.4, 15 mM Fos-Choline-14, 30 mM beta-OG against reservoir solution of 2 M ammonium sulfate, 0.2 M potassium sodium tartrate, 0.1 M sodium citrate, pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.88 57.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.366 α = 90 b = 135.044 β = 91.53 c = 132.449 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 2016-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.886 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 2.35 132.4 94.5 0.101 0.925 7.2 2.8 103631
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 2.35 2.39 0.548 0.715 2.1
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 7AHL 2.35 132.4 98621 5010 94.26 0.1962 0.1939 0.1953 0.2395 0.2404 RANDOM 46.182
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] -1.9 -1.33 -0.03 2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.32 r_dihedral_angle_3_deg 18.75 r_dihedral_angle_4_deg 18.476 r_dihedral_angle_1_deg 6.768 r_angle_refined_deg 2.272 r_chiral_restr 0.174 r_bond_refined_d 0.02 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16415 Nucleic Acid Atoms Solvent Atoms 857 Heterogen Atoms 269
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing