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Methionyl-tRNA synthetase from Staphylococcus aureus in complex with an inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7WPI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 0.05 M Lithium acetate, 0.1 M HEPES 7.5, 25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.25 45.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.181 α = 90 b = 76.758 β = 90 c = 118.751 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2024-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97923 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 46.964 100 0.088 22.4 12.4 37385
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 0.256 9.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2 46.964 37318 1844 99.946 0.197 0.1961 0.2017 0.2185 0.2238 17.93
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] -0.288 0.488 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.176 r_dihedral_angle_4_deg 13.899 r_dihedral_angle_3_deg 11.578 r_dihedral_angle_1_deg 6.013 r_lrange_it 2.84 r_lrange_other 2.557 r_angle_other_deg 2.306 r_angle_refined_deg 1.136 r_mcangle_it 0.698 r_mcangle_other 0.698
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.176 r_dihedral_angle_4_deg 13.899 r_dihedral_angle_3_deg 11.578 r_dihedral_angle_1_deg 6.013 r_lrange_it 2.84 r_lrange_other 2.557 r_angle_other_deg 2.306 r_angle_refined_deg 1.136 r_mcangle_it 0.698 r_mcangle_other 0.698 r_scangle_it 0.412 r_scangle_other 0.412 r_mcbond_it 0.368 r_mcbond_other 0.368 r_symmetry_nbd_other 0.202 r_scbond_it 0.196 r_scbond_other 0.196 r_nbd_refined 0.17 r_nbtor_refined 0.162 r_symmetry_nbd_refined 0.147 r_nbd_other 0.133 r_xyhbond_nbd_refined 0.085 r_symmetry_xyhbond_nbd_refined 0.062 r_symmetry_nbtor_other 0.06 r_chiral_restr 0.048 r_bond_other_d 0.035 r_symmetry_xyhbond_nbd_other 0.013 r_gen_planes_other 0.005 r_gen_planes_refined 0.004 r_bond_refined_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4021 Nucleic Acid Atoms Solvent Atoms 531 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction XDS data scaling MOLREP phasing