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Crystal structure of peptidyl-tRNA hydrolase from Acinetobacter baumannii at 1.00 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6J93
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 12% PEG 1500, 0.1M HEPES, pH 7.5, 20% Glycerol
Crystal Properties Matthews coefficient Solvent content 2 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34 α = 90 b = 66.25 β = 90 c = 76.23 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 2018-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9720 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1 33.15 96.65 0.09 0.04 0.996 11.1 9.5 90567
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1 1.02 98.8 0.79 0.42 0.74 2.4 8.5
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6j93 1 33.147 89426 4520 95.406 0.145 0.1448 0.1569 0.1783 15.225
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] -0.122 0.2 -0.078
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 39.083 r_dihedral_angle_2_deg 34.865 r_dihedral_angle_4_deg 15.941 r_scbond_it 14.984 r_scbond_other 14.984 r_lrange_other 14.698 r_lrange_it 14.603 r_scangle_it 13.717 r_scangle_other 13.716 r_dihedral_angle_3_deg 12.552
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 39.083 r_dihedral_angle_2_deg 34.865 r_dihedral_angle_4_deg 15.941 r_scbond_it 14.984 r_scbond_other 14.984 r_lrange_other 14.698 r_lrange_it 14.603 r_scangle_it 13.717 r_scangle_other 13.716 r_dihedral_angle_3_deg 12.552 r_mcbond_other 12.249 r_mcbond_it 12.242 r_mcangle_it 10.896 r_mcangle_other 10.892 r_dihedral_angle_1_deg 6.564 r_angle_refined_deg 2.514 r_angle_other_deg 1.794 r_symmetry_nbd_refined 0.301 r_xyhbond_nbd_refined 0.246 r_nbd_refined 0.242 r_nbd_other 0.239 r_symmetry_xyhbond_nbd_other 0.234 r_symmetry_nbd_other 0.208 r_symmetry_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.183 r_chiral_restr 0.158 r_symmetry_nbtor_other 0.093 r_bond_refined_d 0.026 r_gen_planes_refined 0.013 r_bond_other_d 0.01 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1496 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing