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Crystal structure of native peptidyl t-RNA hydrolase from Acinetobacter baumannii at 1.38A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JWK
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 38.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.98 α = 90 b = 65.98 β = 90 c = 75.89 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 2013-06-23 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) 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 1.38 25.31 100 34019 34019
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.38 1.4 97.9
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 4JWK 1.38 25.31 34019 34019 1793 99.98 0.13091 0.12978 0.1291 0.15242 0.1517 RANDOM 12.079
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] -0.18 0.09 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.413 r_sphericity_free 24.045 r_dihedral_angle_3_deg 11.125 r_dihedral_angle_4_deg 10.933 r_dihedral_angle_1_deg 5.468 r_sphericity_bonded 5.441 r_long_range_B_refined 2.467 r_long_range_B_other 2.467 r_scangle_other 1.212 r_mcangle_it 1.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.413 r_sphericity_free 24.045 r_dihedral_angle_3_deg 11.125 r_dihedral_angle_4_deg 10.933 r_dihedral_angle_1_deg 5.468 r_sphericity_bonded 5.441 r_long_range_B_refined 2.467 r_long_range_B_other 2.467 r_scangle_other 1.212 r_mcangle_it 1.139 r_mcangle_other 1.139 r_angle_refined_deg 1.117 r_rigid_bond_restr 1.074 r_scbond_it 1.037 r_scbond_other 1.037 r_mcbond_it 0.82 r_mcbond_other 0.819 r_angle_other_deg 0.746 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1496 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 12
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALEPACK data scaling