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Crystal structure of bacterial prolyl-tRNA synthetase in complex with inhibitor PAA-19
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 2.93 58.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.668 α = 90 b = 102.38 β = 90 c = 193.477 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 0.987 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 1.807 96.74 97 0.058 0.058 0.999 19 6.2 131943
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 1.807 1.91 0.416 0.459 0.873 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 1.807 96.739 131856 6653 96.786 0.181 0.18 0.1899 0.2085 0.2154 25.931
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] 1.218 0.025 -1.243
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.631 r_dihedral_angle_3_deg 12.981 r_dihedral_angle_1_deg 6.503 r_dihedral_angle_2_deg 5.499 r_lrange_it 4.781 r_lrange_other 4.676 r_scangle_it 3.631 r_scangle_other 3.631 r_mcangle_it 2.523 r_mcangle_other 2.523
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.631 r_dihedral_angle_3_deg 12.981 r_dihedral_angle_1_deg 6.503 r_dihedral_angle_2_deg 5.499 r_lrange_it 4.781 r_lrange_other 4.676 r_scangle_it 3.631 r_scangle_other 3.631 r_mcangle_it 2.523 r_mcangle_other 2.523 r_scbond_it 2.31 r_scbond_other 2.31 r_mcbond_it 1.747 r_mcbond_other 1.745 r_angle_refined_deg 1.171 r_chiral_restr_other 0.49 r_angle_other_deg 0.42 r_nbd_other 0.264 r_nbd_refined 0.206 r_symmetry_nbd_other 0.201 r_symmetry_nbd_refined 0.198 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.144 r_xyhbond_nbd_refined 0.14 r_symmetry_xyhbond_nbd_other 0.135 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.058 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8722 Nucleic Acid Atoms Solvent Atoms 774 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing