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Crystal structure of Escherichia coli tryptophanyl-tRNA synthetase in complex with an inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8I1Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 0.15 M ammonium sulfate, 0.1 M HEPES pH 7.5, 25% w/v PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.38 48.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.495 α = 90 b = 79.532 β = 105.82 c = 77.651 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS 6M 2024-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97861 SSRF BL19U1
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 1.88 59.16 98.5 0.086 13.6 6.4 57750
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 1.88 1.98 0.653
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.88 59.16 54869 2861 98.8 0.19503 0.19381 0.1966 0.2183 0.2195 RANDOM 25.82
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] -2.27 0.07 1.7 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.028 r_dihedral_angle_4_deg 19.325 r_dihedral_angle_3_deg 12.455 r_dihedral_angle_1_deg 5.435 r_long_range_B_refined 4.166 r_long_range_B_other 4.139 r_scangle_other 3.649 r_scbond_it 2.87 r_scbond_other 2.814 r_mcangle_it 2.563
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.028 r_dihedral_angle_4_deg 19.325 r_dihedral_angle_3_deg 12.455 r_dihedral_angle_1_deg 5.435 r_long_range_B_refined 4.166 r_long_range_B_other 4.139 r_scangle_other 3.649 r_scbond_it 2.87 r_scbond_other 2.814 r_mcangle_it 2.563 r_mcangle_other 2.563 r_angle_other_deg 2.349 r_mcbond_it 2.065 r_mcbond_other 2.064 r_angle_refined_deg 1.742 r_chiral_restr 0.101 r_bond_other_d 0.036 r_bond_refined_d 0.015 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 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 5000 Nucleic Acid Atoms Solvent Atoms 506 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling MOLREP phasing