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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 0.1M Sodium cacodylate pH 6.5; 22% w/v PEG3,350
Crystal Properties Matthews coefficient Solvent content 2.3 46.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.627 α = 90 b = 77.171 β = 90 c = 119.464 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 RIGAKU HyPix-6000HE 2023-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.5 23.631 99.7 0.063 24.32 4.3 19687
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 2.5 2.59 0.218 4.66
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 2.501 23.631 19627 1010 99.715 0.225 0.2231 0.2264 0.256 0.2626 17.295
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] -0.155 -0.008 0.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.596 r_dihedral_angle_3_deg 13.507 r_dihedral_angle_4_deg 11.928 r_dihedral_angle_1_deg 5.05 r_lrange_it 1.463 r_lrange_other 1.368 r_angle_refined_deg 1.132 r_angle_other_deg 1.097 r_mcangle_it 0.468 r_mcangle_other 0.468
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.596 r_dihedral_angle_3_deg 13.507 r_dihedral_angle_4_deg 11.928 r_dihedral_angle_1_deg 5.05 r_lrange_it 1.463 r_lrange_other 1.368 r_angle_refined_deg 1.132 r_angle_other_deg 1.097 r_mcangle_it 0.468 r_mcangle_other 0.468 r_scangle_it 0.273 r_scangle_other 0.273 r_mcbond_it 0.248 r_mcbond_other 0.248 r_symmetry_xyhbond_nbd_refined 0.222 r_symmetry_nbd_other 0.162 r_nbtor_refined 0.157 r_nbd_refined 0.15 r_scbond_it 0.136 r_scbond_other 0.136 r_nbd_other 0.124 r_xyhbond_nbd_refined 0.115 r_symmetry_nbtor_other 0.083 r_symmetry_nbd_refined 0.071 r_chiral_restr 0.035 r_bond_refined_d 0.002 r_bond_other_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4023 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction SCALA data scaling MOLREP phasing