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Crystal structure of a dimeric Piptidyl t-RNA hydrolase from Acinetobacter baumannii at 1.50 A resolution reveals an inhibited form.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YN4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 20% PEG 1500, 0.1M HEPES, pH 7.5, 22% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.51 51.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.58 α = 90 b = 98.54 β = 90 c = 123.67 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 2019-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.97 RRCAT INDUS-2 PX-BL21
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.5 38.56 99.97 0.1 0.108 0.042 0.99 11.2 6.5 68761 10.37
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 99.92 0.53 0.58 0.22 0.86 3.4 6.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5YN4 1.5 33.3 1.35 68759 1405 99.98 0.1701 0.1696 0.1698 0.1968 0.1968 15.2
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.5339 f_angle_d 0.8213 f_chiral_restr 0.0562 f_bond_d 0.0057 f_plane_restr 0.0051
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2952 Nucleic Acid Atoms Solvent Atoms 622 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling MOLREP phasing