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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 1.95 36.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.961 α = 90 b = 74.132 β = 90 c = 116.719 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 2025-01-10 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 26.981 99.9 0.16 12.3 9 16849
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 0.39 5.1
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 26.981 16787 828 99.845 0.231 0.2297 0.2322 0.257 0.2627 16.49
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] -1.807 -0.073 1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.198 r_dihedral_angle_3_deg 16.548 r_dihedral_angle_4_deg 15.689 r_dihedral_angle_1_deg 5.74 r_angle_other_deg 2.319 r_lrange_it 1.479 r_lrange_other 1.452 r_angle_refined_deg 1.182 r_mcangle_it 0.499 r_mcangle_other 0.499
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.198 r_dihedral_angle_3_deg 16.548 r_dihedral_angle_4_deg 15.689 r_dihedral_angle_1_deg 5.74 r_angle_other_deg 2.319 r_lrange_it 1.479 r_lrange_other 1.452 r_angle_refined_deg 1.182 r_mcangle_it 0.499 r_mcangle_other 0.499 r_mcbond_it 0.263 r_mcbond_other 0.263 r_scangle_it 0.259 r_scangle_other 0.259 r_nbd_other 0.237 r_symmetry_nbd_refined 0.231 r_symmetry_nbd_other 0.201 r_nbd_refined 0.163 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.128 r_scbond_it 0.124 r_scbond_other 0.124 r_symmetry_xyhbond_nbd_refined 0.097 r_symmetry_xyhbond_nbd_other 0.067 r_symmetry_nbtor_other 0.065 r_chiral_restr 0.043 r_bond_other_d 0.035 r_gen_planes_other 0.004 r_gen_planes_refined 0.003 r_bond_refined_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4054 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction SCALA data scaling MOLREP phasing