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Crystal structure of threonyl-tRNA synthetase (ThrRS) from Salmonella enterica in complex with an inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6L2Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.24 M lithium acetate pH 7.5, 18% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.43 49.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.793 α = 90 b = 101.796 β = 90 c = 105.633 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 2019-07-30 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 2.5 50 99.6 0.039 25.8 5 32934
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 2.5 2.64 0.089 10.9
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 6L2Q 2.5 50 31158 1603 99.1 0.21706 0.21475 0.2176 0.26126 0.2638 RANDOM 23.056
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] 1.63 -1.38 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.524 r_dihedral_angle_3_deg 15.002 r_dihedral_angle_4_deg 11.143 r_dihedral_angle_1_deg 5.369 r_long_range_B_refined 1.84 r_long_range_B_other 1.757 r_angle_refined_deg 1.046 r_angle_other_deg 0.871 r_mcangle_it 0.773 r_mcangle_other 0.773
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.524 r_dihedral_angle_3_deg 15.002 r_dihedral_angle_4_deg 11.143 r_dihedral_angle_1_deg 5.369 r_long_range_B_refined 1.84 r_long_range_B_other 1.757 r_angle_refined_deg 1.046 r_angle_other_deg 0.871 r_mcangle_it 0.773 r_mcangle_other 0.773 r_mcbond_it 0.407 r_mcbond_other 0.407 r_scangle_other 0.407 r_scbond_it 0.197 r_scbond_other 0.197 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6483 Nucleic Acid Atoms Solvent Atoms 386 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction SCALA data scaling MOLREP phasing