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Crystal structure of peptidyl-tRNA hydrolase from Acinetobacter baumannii at 0.99 A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5Y9A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 HEPES, PEG 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298 K
Crystal Properties Matthews coefficient Solvent content 2.01 38.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.139 α = 90 b = 65.976 β = 90 c = 76.011 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 PSI PILATUS 6M 2018-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97201 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 0.99 49.83 92 0.059 0.063 0.025 0.99 9.8 5.64 86816
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.99 1.01 29.3 2.3 2.89 1.71 0.11 0.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5Y9A 0.99 49.83 86816 1794 92 0.12993 0.12972 0.1297 0.13932 0.1401 RANDOM 16.252
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] -0.18 0.17 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.419 r_dihedral_angle_4_deg 17.581 r_rigid_bond_restr 16.684 r_dihedral_angle_3_deg 12.379 r_scangle_other 6.538 r_scbond_other 6.228 r_scbond_it 6.218 r_long_range_B_refined 6.197 r_long_range_B_other 6.195 r_dihedral_angle_1_deg 6.194
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.419 r_dihedral_angle_4_deg 17.581 r_rigid_bond_restr 16.684 r_dihedral_angle_3_deg 12.379 r_scangle_other 6.538 r_scbond_other 6.228 r_scbond_it 6.218 r_long_range_B_refined 6.197 r_long_range_B_other 6.195 r_dihedral_angle_1_deg 6.194 r_mcbond_other 4.55 r_mcbond_it 4.548 r_mcangle_it 4.147 r_mcangle_other 4.145 r_angle_refined_deg 2.096 r_angle_other_deg 0.716 r_chiral_restr 0.123 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1496 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing