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Crystal structure of peptidyl-tRNA hydrolase from Acinetobacter baumannii with 12% PEG 1500 at 1.55 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 12% PEG 1500, 0.1M HEPES PH 7.5
Crystal Properties Matthews coefficient Solvent content 1.98 37.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.795 α = 90 b = 65.849 β = 90 c = 75.746 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 PILATUS 2M 2018-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96600 ESRF MASSIF-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 1.55 37.9 92.08 0.11 0.138 0.068 0.987 5.9 3.78 25090 7.1
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 1.55 1.58 0.56 0.66 0.33 0.692 2.2
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 1.55 37.9 21953 1150 92.08 0.25381 0.25262 0.2613 0.27691 0.2822 RANDOM 9.376
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] -0.25 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.185 r_dihedral_angle_4_deg 12.942 r_dihedral_angle_3_deg 12.658 r_dihedral_angle_1_deg 6.271 r_long_range_B_refined 4.785 r_long_range_B_other 4.136 r_scangle_other 2.224 r_angle_refined_deg 1.637 r_angle_other_deg 1.512 r_scbond_it 1.409
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.185 r_dihedral_angle_4_deg 12.942 r_dihedral_angle_3_deg 12.658 r_dihedral_angle_1_deg 6.271 r_long_range_B_refined 4.785 r_long_range_B_other 4.136 r_scangle_other 2.224 r_angle_refined_deg 1.637 r_angle_other_deg 1.512 r_scbond_it 1.409 r_scbond_other 1.405 r_mcangle_other 1.357 r_mcangle_it 1.355 r_mcbond_it 0.877 r_mcbond_other 0.829 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1496 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing