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Methionyl-tRNA synthetase from Staphylococcus aureus complexed with a fragment M2-80 and ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7WPM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 300 Sodium cacodylate, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.27 45.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.993 α = 90 b = 76.536 β = 90 c = 118.642 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 EIGER2 S 9M 2021-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97914 SSRF BL02U1
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 2.26 64.31 93.2 0.07 12.2 3.4 24773
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 2.26 2.409 98.1 0.54 3
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 7WPM 2.26 64.31 23442 1272 92.92 0.2236 0.2211 0.2257 0.2673 0.261 RANDOM 45.547
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] 2.36 -1.35 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.415 r_dihedral_angle_4_deg 20.266 r_dihedral_angle_3_deg 18.46 r_dihedral_angle_1_deg 5.859 r_angle_refined_deg 1.213 r_angle_other_deg 1.158 r_chiral_restr 0.055 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.415 r_dihedral_angle_4_deg 20.266 r_dihedral_angle_3_deg 18.46 r_dihedral_angle_1_deg 5.859 r_angle_refined_deg 1.213 r_angle_other_deg 1.158 r_chiral_restr 0.055 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3903 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 63
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction MOLREP phasing