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Crystal Structure of Peptidyl-tRNA hydrolase from Acinetobacter baumannii at 1.86 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PTH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 310 0.2M HEPES Buffer, 25% PEG10000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Crystal Properties Matthews coefficient Solvent content 2.59 52.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.255 α = 90 b = 57.864 β = 90 c = 109.744 γ = 90
Symmetry Space Group P 21 2 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 2012-05-18 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 1.86 57.8 99.1 0.062 11.6 18987 17986
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 1.86 1.93 99.4 0.573 1.7 18987
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2PTH 1.86 57.8 18987 17986 976 99.43 0.17785 0.17518 0.1745 0.22795 0.2264 RANDOM 27.029
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] -1.12 1.55 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.431 r_dihedral_angle_3_deg 15.086 r_dihedral_angle_4_deg 8.841 r_dihedral_angle_1_deg 6.051 r_angle_refined_deg 2.036 r_chiral_restr 0.151 r_bond_refined_d 0.021 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1475 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 44
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling