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Crystal structure of native unbound peptidyl tRNA hydrolase from Acinetobacter baumannii at 1.36 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WH4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 50mM HEPES, PEG 400, PEG 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2 38.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.98 α = 90 b = 65.97 β = 90 c = 75.88 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 CCD MARRESEARCH Mirror 2013-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.36 25.32 99.9 20.2 4.2 37477
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 1.395
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 3WH4 1.36 25.32 35544 1871 99.93 0.10807 0.10621 0.1074 0.14449 0.146 RANDOM 14.678
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.582 r_dihedral_angle_2_deg 34.793 r_dihedral_angle_4_deg 14.868 r_sphericity_bonded 13.731 r_dihedral_angle_3_deg 12.882 r_rigid_bond_restr 9.097 r_long_range_B_refined 7.279 r_long_range_B_other 7.069 r_dihedral_angle_1_deg 5.9 r_mcangle_it 5.497
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.582 r_dihedral_angle_2_deg 34.793 r_dihedral_angle_4_deg 14.868 r_sphericity_bonded 13.731 r_dihedral_angle_3_deg 12.882 r_rigid_bond_restr 9.097 r_long_range_B_refined 7.279 r_long_range_B_other 7.069 r_dihedral_angle_1_deg 5.9 r_mcangle_it 5.497 r_mcangle_other 5.495 r_scangle_other 5.049 r_scbond_other 4.289 r_scbond_it 4.288 r_mcbond_other 3.964 r_mcbond_it 3.96 r_angle_other_deg 2.799 r_angle_refined_deg 2.21 r_chiral_restr 0.157 r_bond_refined_d 0.031 r_gen_planes_other 0.013 r_gen_planes_refined 0.012 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1496 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing