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Crystal structure of PEG-1500 crystallized Peptidyl-tRNA Hydrolase from Acinetobacter baumannii at 1.5 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FOP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 100mM HEPES, 15% PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.62 53.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.025 α = 90 b = 34.383 β = 90 c = 58.659 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2018-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9095 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) 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 1.57 39.93 99.5 0.151 0.145 8.7 12 24836 26.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.57 1.63 99.5 0.151 0.145 8.7 12
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4FOP 1.57 39.93 23593 1242 78.19 0.17177 0.17001 0.20544 0.2134 RANDOM 30.875
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] -0.21 -1.16 1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.73 r_dihedral_angle_4_deg 13.073 r_dihedral_angle_3_deg 12.661 r_long_range_B_refined 7.453 r_long_range_B_other 7.453 r_dihedral_angle_1_deg 6.809 r_scangle_other 5.833 r_scbond_it 3.906 r_scbond_other 3.906 r_mcangle_it 3.507
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.73 r_dihedral_angle_4_deg 13.073 r_dihedral_angle_3_deg 12.661 r_long_range_B_refined 7.453 r_long_range_B_other 7.453 r_dihedral_angle_1_deg 6.809 r_scangle_other 5.833 r_scbond_it 3.906 r_scbond_other 3.906 r_mcangle_it 3.507 r_mcangle_other 3.505 r_mcbond_it 2.608 r_mcbond_other 2.571 r_angle_refined_deg 1.888 r_angle_other_deg 1.072 r_chiral_restr 0.125 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1475 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALEPACK data scaling MOLREP phasing