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Crystal structure of bacterial prolyl-tRNA synthetase in complex with inhibitor PAA-5
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 acetate, 0.1 M BIS-TRIS, 26% PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.89 57.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.584 α = 90 b = 102.622 β = 90 c = 194.084 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 2019-05-27 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) 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 2.35 97.05 99 0.126 0.963 12.6 6.4 55512
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 2.35 2.39 89.2 0.911
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 2.45 49.656 55512 2791 99.795 0.216 0.2141 0.2484 0.2303 39.717
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] 1.739 -1.726 -0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.874 r_dihedral_angle_3_deg 12.739 r_dihedral_angle_1_deg 6.349 r_lrange_it 3.399 r_lrange_other 3.399 r_dihedral_angle_2_deg 3.364 r_mcangle_it 2.166 r_mcangle_other 2.166 r_scangle_it 2.002 r_scangle_other 2.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.874 r_dihedral_angle_3_deg 12.739 r_dihedral_angle_1_deg 6.349 r_lrange_it 3.399 r_lrange_other 3.399 r_dihedral_angle_2_deg 3.364 r_mcangle_it 2.166 r_mcangle_other 2.166 r_scangle_it 2.002 r_scangle_other 2.002 r_mcbond_it 1.258 r_mcbond_other 1.257 r_scbond_it 1.131 r_scbond_other 1.131 r_angle_refined_deg 0.811 r_angle_other_deg 0.289 r_symmetry_nbd_other 0.19 r_nbd_refined 0.186 r_nbtor_refined 0.167 r_nbd_other 0.166 r_symmetry_nbd_refined 0.107 r_xyhbond_nbd_refined 0.105 r_symmetry_xyhbond_nbd_other 0.078 r_symmetry_nbtor_other 0.077 r_symmetry_xyhbond_nbd_refined 0.076 r_chiral_restr 0.038 r_chiral_restr_other 0.006 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8652 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction MOLREP phasing