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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 3B07 PDB entry 3B07
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 298 6.7 mg/mL LukF-PV, 6.3 mg/mL LukS-PV, 10 mM sodium acetate, pH 5.4, 15 mM Fos-Choline-14, 40 mM beta-OG against reservoir solution of 0.16 M magnesium formate
Crystal Properties Matthews coefficient Solvent content 3.17 61.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.097 α = 90 b = 139.097 β = 90 c = 246.77 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 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 2.04 38.7 99.9 0.098 0.956 6.6 12.8 76882
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 2.04 2.09 0.981 0.754 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 3B07 2.04 38.69 72993 3889 99.86 0.1845 0.1823 0.1826 0.225 0.2254 RANDOM 44.123
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] -1.38 -1.38 2.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.654 r_dihedral_angle_4_deg 20.674 r_dihedral_angle_3_deg 16.567 r_dihedral_angle_1_deg 8.04 r_angle_refined_deg 2.239 r_chiral_restr 0.167 r_bond_refined_d 0.015 r_gen_planes_refined 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6646 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 159
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing