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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 6U49 PDB entry 6U49
Crystallization Crystalization Experiments 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 Matthews coefficient Solvent content 2.86 56.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.174 α = 90 b = 134.616 β = 91.84 c = 130.697 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 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 2.49 37.8 96.5 0.061 0.968 10.2 3.4 87452
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 2.49 2.56 98.1 0.515 0.864 2.4 3.4
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 6U49 2.49 37.8 83195 4257 96.2 0.2139 0.2121 0.2135 0.2495 0.2509 RANDOM 75.524
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] -0.6 0.65 -1.97 2.53
RMS Deviations 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 Non-Hydrogen Atoms Number Protein Atoms 16380 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 320
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing