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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 2.09 41.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.276 α = 90 b = 72.716 β = 90 c = 118.71 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 2.09 46.02 99.7 0.153 0.167 0.065 0.991 9.4 6.5 30973
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 2.09 2.15 97 0.508 0.557 0.225 0.872 6
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 2.09 46.02 29369 1544 99.58 0.2145 0.2126 0.2207 0.2494 0.2546 RANDOM 19.778
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] 2.08 -0.21 -1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.862 r_dihedral_angle_4_deg 15.428 r_dihedral_angle_3_deg 14.57 r_dihedral_angle_1_deg 5.957 r_angle_refined_deg 1.183 r_angle_other_deg 1.142 r_chiral_restr 0.049 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.862 r_dihedral_angle_4_deg 15.428 r_dihedral_angle_3_deg 14.57 r_dihedral_angle_1_deg 5.957 r_angle_refined_deg 1.183 r_angle_other_deg 1.142 r_chiral_restr 0.049 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4182 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing