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Crystal structure of Peptidyl-tRNA hydrolase from Pseudomonas aeruginosa with 5-azacytidine at 1.89 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, Isopropanol, HEPES buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.23 44.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.111 α = 90 b = 64.111 β = 90 c = 156.62 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) R Sym I (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 1.89 32.08 99.9 0.075 51.7 16071 16071
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.92 99.9 0.491 4.5
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4JC4 1.89 32.08 15212 799 99.93 0.18897 0.18642 0.23803 0.223 RANDOM 28.774
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] 0.4 0.4 0.4 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.703 r_dihedral_angle_4_deg 14.817 r_dihedral_angle_3_deg 14.332 r_long_range_B_refined 5.59 r_long_range_B_other 5.586 r_dihedral_angle_1_deg 4.884 r_angle_other_deg 3.648 r_scangle_other 2.577 r_mcangle_other 2.05 r_mcangle_it 2.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.703 r_dihedral_angle_4_deg 14.817 r_dihedral_angle_3_deg 14.332 r_long_range_B_refined 5.59 r_long_range_B_other 5.586 r_dihedral_angle_1_deg 4.884 r_angle_other_deg 3.648 r_scangle_other 2.577 r_mcangle_other 2.05 r_mcangle_it 2.049 r_scbond_it 1.55 r_scbond_other 1.544 r_angle_refined_deg 1.305 r_mcbond_it 1.226 r_mcbond_other 1.222 r_chiral_restr 0.109 r_bond_refined_d 0.014 r_gen_planes_other 0.006 r_gen_planes_refined 0.005 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1467 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 23
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling