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Crystal structure of Arg119Gln mutant of Peptidyl-tRNA Hydrolase from Acinetobacter Baumannii at 1.49 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LWQ
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 2.01 38.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.088 α = 90 b = 65.834 β = 90 c = 76.121 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 77 CCD MARRESEARCH Mirror 2013-11-29 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 1.49 50 99.1 0.067 32.9 26963 26963
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 1.49 1.52 94.4 0.457 2.1 26963
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 4LWQ 1.49 49.79 26963 1435 99.13 0.15967 0.15788 0.1664 0.19243 0.2008 RANDOM 18.904
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] -0.31 0.2 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.176 r_dihedral_angle_4_deg 15.97 r_dihedral_angle_3_deg 14.458 r_scangle_it 6.157 r_dihedral_angle_1_deg 5.88 r_scbond_it 3.848 r_mcangle_it 2.491 r_angle_refined_deg 2.429 r_mcbond_it 1.539 r_chiral_restr 0.172
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.176 r_dihedral_angle_4_deg 15.97 r_dihedral_angle_3_deg 14.458 r_scangle_it 6.157 r_dihedral_angle_1_deg 5.88 r_scbond_it 3.848 r_mcangle_it 2.491 r_angle_refined_deg 2.429 r_mcbond_it 1.539 r_chiral_restr 0.172 r_bond_refined_d 0.029 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1494 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 16
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling