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Crystal structure of Peptidyl- tRNA Hydrolase from Acinetobacter baumannii at 1.78 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 6.5 298 0.2 HEPES buffer, 25% PEG 10000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.62 53.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.54 α = 90 b = 58.22 β = 90 c = 109.18 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 2012-05-05 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 Merge 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 1.78 58.2 99.7 0.113 14.5 20636 20636
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.88 99.3 0.611 2.3
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 (All) 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 2PTH 1.78 28.13 20636 20636 1113 99.38 0.17123 0.17018 0.16876 0.1963 0.1852 RANDOM 23.12
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] -1.38 2.02 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.853 r_dihedral_angle_3_deg 14.434 r_dihedral_angle_4_deg 8.92 r_dihedral_angle_1_deg 5.636 r_scangle_it 4.42 r_scbond_it 3.079 r_mcangle_it 1.971 r_angle_refined_deg 1.843 r_mcbond_it 1.331 r_chiral_restr 0.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.853 r_dihedral_angle_3_deg 14.434 r_dihedral_angle_4_deg 8.92 r_dihedral_angle_1_deg 5.636 r_scangle_it 4.42 r_scbond_it 3.079 r_mcangle_it 1.971 r_angle_refined_deg 1.843 r_mcbond_it 1.331 r_chiral_restr 0.187 r_bond_refined_d 0.021 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1476 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 44
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling