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Crystal structure of Piptidyl t-RNA hydrolase from Acinetobacter baumannii with bound NaCl at the substrate binding site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6J93
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 12% PEG 1500, 0.1M HEPES, pH 7.5, 15% Glycerol
Crystal Properties Matthews coefficient Solvent content 2 38.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.961 α = 90 b = 66.099 β = 90 c = 75.825 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 100 CCD MARMOSAIC 225 mm CCD 2019-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.9795 RRCAT INDUS-2 PX-BL21
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.94 31.01 94.03 0.043 0.996 26.18 2.89 12479
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 2.05 91.1 0.049 0.996 21.11 2.72
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6J93 1.94 31.01 11218 1261 94.025 0.131 0.1268 0.1414 0.1638 0.1743 13.263
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] -0.037 0.024 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.05 r_dihedral_angle_4_deg 19.24 r_dihedral_angle_3_deg 14.009 r_dihedral_angle_1_deg 6.623 r_lrange_it 6.136 r_lrange_other 6.134 r_scangle_it 3.678 r_scangle_other 3.676 r_mcangle_other 2.438 r_mcangle_it 2.437
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.05 r_dihedral_angle_4_deg 19.24 r_dihedral_angle_3_deg 14.009 r_dihedral_angle_1_deg 6.623 r_lrange_it 6.136 r_lrange_other 6.134 r_scangle_it 3.678 r_scangle_other 3.676 r_mcangle_other 2.438 r_mcangle_it 2.437 r_scbond_it 2.319 r_scbond_other 2.318 r_angle_refined_deg 1.661 r_mcbond_it 1.513 r_mcbond_other 1.502 r_angle_other_deg 1.457 r_nbd_other 0.283 r_symmetry_xyhbond_nbd_other 0.214 r_symmetry_nbd_refined 0.213 r_nbd_refined 0.21 r_symmetry_nbd_other 0.201 r_xyhbond_nbd_refined 0.193 r_symmetry_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.161 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1496 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing