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Structure of Peptidyl- tRNA Hydrolase from Acinetobacter baumannii at 1.90 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 0.2M HEPES buffer, 25% PEG 10000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.62 53.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.56 α = 90 b = 58.22 β = 90 c = 109.25 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 1.9 58.22 99.8 0.1 16.5 18051 18051
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 1.9 2 99.6 0.537 4.2
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 1.9 58.22 18051 17095 919 99.55 0.16932 0.16736 0.15551 0.19226 0.1841 RANDOM 23.587
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] -1.46 1.92 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.602 r_dihedral_angle_3_deg 15.08 r_dihedral_angle_4_deg 13.469 r_scangle_it 5.968 r_dihedral_angle_1_deg 5.938 r_scbond_it 3.883 r_mcangle_it 2.465 r_angle_refined_deg 1.822 r_mcbond_it 1.503 r_chiral_restr 0.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.602 r_dihedral_angle_3_deg 15.08 r_dihedral_angle_4_deg 13.469 r_scangle_it 5.968 r_dihedral_angle_1_deg 5.938 r_scbond_it 3.883 r_mcangle_it 2.465 r_angle_refined_deg 1.822 r_mcbond_it 1.503 r_chiral_restr 0.193 r_bond_refined_d 0.016 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1476 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 44
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling