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Crystal structure of bacterial prolyl-tRNA synthetase in complex with inhibitor PAA-38
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UCM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.9 57.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.484 α = 90 b = 103.06 β = 90 c = 194.095 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 2023-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.82 97.05 99.1 0.056 0.061 0.999 20.3 6.1 132338
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.92 0.448 0.51 0.866 2.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.824 97.048 132241 6624 99.022 0.213 0.2112 0.2221 0.2412 0.2517 25.033
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] 2.09 -1.029 -1.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.278 r_dihedral_angle_3_deg 13.588 r_dihedral_angle_1_deg 6.473 r_dihedral_angle_2_deg 4.049 r_lrange_it 3.51 r_lrange_other 3.393 r_scangle_it 1.857 r_scangle_other 1.857 r_mcangle_it 1.725 r_mcangle_other 1.725
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.278 r_dihedral_angle_3_deg 13.588 r_dihedral_angle_1_deg 6.473 r_dihedral_angle_2_deg 4.049 r_lrange_it 3.51 r_lrange_other 3.393 r_scangle_it 1.857 r_scangle_other 1.857 r_mcangle_it 1.725 r_mcangle_other 1.725 r_scbond_it 1.104 r_scbond_other 1.104 r_angle_refined_deg 1.047 r_mcbond_it 1.032 r_mcbond_other 1.031 r_angle_other_deg 0.376 r_symmetry_nbd_other 0.201 r_nbd_refined 0.197 r_nbd_other 0.183 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.162 r_xyhbond_nbd_refined 0.126 r_symmetry_nbd_refined 0.09 r_symmetry_nbtor_other 0.079 r_chiral_restr_other 0.072 r_chiral_restr 0.049 r_symmetry_xyhbond_nbd_other 0.03 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 8681 Nucleic Acid Atoms Solvent Atoms 807 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling MOLREP phasing