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Crystal structure of human prolyl-tRNA synthetase in complex with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HVC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.4 289 0.2 M magnesium chloride, 0.1 M Tris pH 8.4, 20% PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.28 45.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.602 α = 90 b = 92.157 β = 108.629 c = 86.621 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 PILATUS3 6M 2021-10-17 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) CC (Half) 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 2.55 50 99.6 0.195 0.975 26.4 3.4 34745
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 2.55 2.59 99.4 0.119 0.975 7.85 3.6
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.553 46.121 34607 1797 99.46 0.205 0.2023 0.2496 0.2673 44.659
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] -1.265 -0.9 3.652 -1.451
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.784 r_dihedral_angle_6_deg 14.673 r_dihedral_angle_1_deg 5.82 r_dihedral_angle_2_deg 3.855 r_lrange_it 2.234 r_lrange_other 2.234 r_angle_refined_deg 1.067 r_scangle_it 0.942 r_scangle_other 0.942 r_mcangle_it 0.862
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.784 r_dihedral_angle_6_deg 14.673 r_dihedral_angle_1_deg 5.82 r_dihedral_angle_2_deg 3.855 r_lrange_it 2.234 r_lrange_other 2.234 r_angle_refined_deg 1.067 r_scangle_it 0.942 r_scangle_other 0.942 r_mcangle_it 0.862 r_mcangle_other 0.862 r_scbond_it 0.56 r_scbond_other 0.56 r_mcbond_it 0.503 r_mcbond_other 0.503 r_angle_other_deg 0.41 r_symmetry_nbd_other 0.201 r_nbd_refined 0.189 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.165 r_nbd_other 0.157 r_symmetry_nbd_refined 0.104 r_symmetry_xyhbond_nbd_other 0.099 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_refined 0.058 r_chiral_restr 0.055 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7362 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing