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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 4YHD PDB entry 4YHD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 10 mg/mL protein in 10 mM sodium acetate, pH 5.4, 5 mM Fos-Choline-14, 40 mM beta-OG, 0.4 mM Deoxy-Big CHAP against reservoir solution of 1.5 M ammonium sulfate, 0.25 M potassium sodium tartrate, 0.1 M sodium citrate, pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.9 62.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.18 α = 90 b = 136.18 β = 90 c = 166.045 γ = 90
Symmetry Space Group I 4 2 2
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 2017-12-13 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 2.79 43.82 99.8 0.135 0.956 5.4 12.7 19666
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 2.8 2.87 99.1 0.912 0.716 2.4 10.4
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 4YHD 2.79 43.82 18691 975 99.34 0.1996 0.1971 0.198 0.246 0.2456 RANDOM 71.638
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] -0.76 -0.76 1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.801 r_dihedral_angle_4_deg 22.954 r_dihedral_angle_3_deg 18.288 r_dihedral_angle_1_deg 7.233 r_angle_refined_deg 0.956 r_chiral_restr 0.078 r_bond_refined_d 0.003 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4114 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing