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Threonyl-tRNA synthetase from Salmonella enterica in the apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HWP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 293 0.22 M lithium acetate pH 7.0, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.37 48.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.988 α = 90 b = 101.859 β = 90 c = 106.047 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 PILATUS3 6M 2018-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.987 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.3 50 97.8 0.11 0.121 0.049 22.035 6.2 40001
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 99 0.49 0.911 5.3
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 4HWP 2.3 50 37882 2065 97.29 0.2227 0.2205 0.2221 0.2614 0.2596 RANDOM 51.017
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] 3.12 -1.17 -1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.534 r_dihedral_angle_4_deg 14.975 r_dihedral_angle_3_deg 14.005 r_dihedral_angle_1_deg 5.488 r_angle_refined_deg 1.07 r_angle_other_deg 0.875 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_bond_other_d 0.006 r_gen_planes_refined 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.534 r_dihedral_angle_4_deg 14.975 r_dihedral_angle_3_deg 14.005 r_dihedral_angle_1_deg 5.488 r_angle_refined_deg 1.07 r_angle_other_deg 0.875 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_bond_other_d 0.006 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6480 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction MOLREP phasing