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Methionyl-tRNA synthetase from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QRE
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 1.98 37.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.728 α = 90 b = 68.987 β = 90 c = 117.404 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 2020-12-05 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 2.65 59.73 96 0.03 17.8 3.6 14046
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 2.65 2.74 0.07 8.7
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 4QRE 2.65 59.48 13341 705 95.77 0.2201 0.2173 0.2225 0.2739 0.2771 RANDOM 21.23
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] 1.76 -0.52 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.56 r_dihedral_angle_3_deg 16.116 r_dihedral_angle_4_deg 15.874 r_dihedral_angle_1_deg 5.39 r_angle_other_deg 3.781 r_angle_refined_deg 1.155 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.56 r_dihedral_angle_3_deg 16.116 r_dihedral_angle_4_deg 15.874 r_dihedral_angle_1_deg 5.39 r_angle_other_deg 3.781 r_angle_refined_deg 1.155 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_gen_planes_other 0.004 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3960 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction CrysalisPro data reduction MOLREP phasing