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Methionyl-tRNA synthetase from Staphylococcus aureus complexed with a fragment and ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7WPK
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 2.15 42.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.888 α = 90 b = 71.376 β = 90 c = 120.815 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) Rrim I (All) Rpim I (All) 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 2.4 120.82 99.9 0.113 0.124 0.05 0.997 13.1 6 21257
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 100 0.613 0.674 0.278 0.845 5.7
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 7WPK 2.4 61.45 20145 1051 99.78 0.2142 0.2131 0.2178 0.2357 0.2308 RANDOM 36.589
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] -2.71 4.48 -1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.076 r_dihedral_angle_3_deg 16.091 r_dihedral_angle_4_deg 13.321 r_dihedral_angle_1_deg 5.424 r_angle_refined_deg 1.148 r_angle_other_deg 0.93 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.076 r_dihedral_angle_3_deg 16.091 r_dihedral_angle_4_deg 13.321 r_dihedral_angle_1_deg 5.424 r_angle_refined_deg 1.148 r_angle_other_deg 0.93 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4142 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction autoPROC data reduction MOLREP phasing