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Threonyl-tRNA synthetase from Salmonella enterica in complex with an inhibitor
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 7 293 0.22 M lithium acetate pH 7.0, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.42 49.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.231 α = 90 b = 101.917 β = 90 c = 105.641 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 2019-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.542
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 2.3 22.18 99.3 0.052 13.1 3.8 41697
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 2.3 2.42 99.7 0.161 4.3 2.8
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 22.18 39447 2147 98.9 0.2117 0.2094 0.2132 0.2542 0.2552 RANDOM 30.339
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] 1.36 -1.57 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.945 r_dihedral_angle_3_deg 12.782 r_dihedral_angle_4_deg 9.462 r_dihedral_angle_1_deg 5.585 r_angle_refined_deg 1.108 r_angle_other_deg 0.883 r_chiral_restr 0.062 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 33.945 r_dihedral_angle_3_deg 12.782 r_dihedral_angle_4_deg 9.462 r_dihedral_angle_1_deg 5.585 r_angle_refined_deg 1.108 r_angle_other_deg 0.883 r_chiral_restr 0.062 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 6501 Nucleic Acid Atoms Solvent Atoms 435 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction CrysalisPro data reduction MOLREP phasing