☰ Navigation Tabs
Crystal structure at atomic resolution reveals the catalytic mechanism in peptidyl-tRNA hydrolase from Acinetobacter baumannii.
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 12% PEG 1500, 0.1M HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid), pH 7.5, 20% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.01 38.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.964 α = 90 b = 66.194 β = 90 c = 75.983 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 0.97199 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 1.02 49.92 88.37 0.093 0.039 0.998 8.45 8.3 73420
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 1.022 1.049 2.236 0.983 0.243 0.756
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 1.02 49.91 73420 3778 88.37 0.13772 0.13671 0.1373 0.15726 0.1608 RANDOM 13.758
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] -0.79 0.58 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.557 r_dihedral_angle_3_deg 12.791 r_dihedral_angle_4_deg 12.316 r_rigid_bond_restr 11.258 r_scbond_other 8.2 r_scbond_it 8.199 r_scangle_other 6.475 r_long_range_B_refined 6.308 r_long_range_B_other 6.207 r_dihedral_angle_1_deg 6.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.557 r_dihedral_angle_3_deg 12.791 r_dihedral_angle_4_deg 12.316 r_rigid_bond_restr 11.258 r_scbond_other 8.2 r_scbond_it 8.199 r_scangle_other 6.475 r_long_range_B_refined 6.308 r_long_range_B_other 6.207 r_dihedral_angle_1_deg 6.099 r_mcangle_other 2.159 r_mcangle_it 2.158 r_angle_refined_deg 1.897 r_mcbond_other 1.868 r_mcbond_it 1.866 r_angle_other_deg 0.745 r_chiral_restr 0.115 r_bond_refined_d 0.018 r_gen_planes_refined 0.012 r_bond_other_d 0.007 r_gen_planes_other 0.003 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 233 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing