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Crystal structure of Peptidyl-tRNA hydrolase from Pseudomonas aeruginosa at 1.5 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JC4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 PEG 4000, 5% isoproponal, 100mM HEPES buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.21 44.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.115 α = 90 b = 64.115 β = 90 c = 155.312 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD MARRESEARCH Mirror 2013-11-02 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 1.5 29.64 99.8 50.3 31169 31169
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 1.5 1.53 99.7 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 4JC4 1.5 29.64 29552 1571 99.86 0.18206 0.18004 0.1805 0.22027 0.2214 RANDOM 24.75
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] 0.09 0.09 0.09 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.959 r_dihedral_angle_4_deg 14.041 r_dihedral_angle_3_deg 13.85 r_long_range_B_refined 6.924 r_long_range_B_other 6.62 r_dihedral_angle_1_deg 5.624 r_scangle_other 4.46 r_angle_other_deg 3.674 r_mcangle_other 3.057 r_mcangle_it 3.047
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.959 r_dihedral_angle_4_deg 14.041 r_dihedral_angle_3_deg 13.85 r_long_range_B_refined 6.924 r_long_range_B_other 6.62 r_dihedral_angle_1_deg 5.624 r_scangle_other 4.46 r_angle_other_deg 3.674 r_mcangle_other 3.057 r_mcangle_it 3.047 r_scbond_it 3.023 r_scbond_other 3.017 r_mcbond_it 2.166 r_mcbond_other 2.141 r_angle_refined_deg 1.926 r_chiral_restr 0.127 r_bond_refined_d 0.021 r_gen_planes_other 0.019 r_gen_planes_refined 0.011 r_bond_other_d 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 1467 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling