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Crystal structure of full-length peptidyl-tRNA hydrolase from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z2I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 293.15 25% (W/V) PEG 8000, 0.1M HEPES pH 7.5
5% (V/V) 2-propanol
Crystal Properties Matthews coefficient Solvent content 2.15 42.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.581 α = 90 b = 39.003 β = 90 c = 123.818 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 PIXEL DECTRIS PILATUS3 6M Vertical CRL/ Horizontal Eliptical mirror 2021-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.976254 ESRF ID30B
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 1.937 37.201 98.61 0.149 0.159 0.055 0.996 11.4 8 13646 18.92
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 1.937 1.97 87.7 0.72 0.78 0.29 0.887 2.5 6.3
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 2Z2I 1.94 37.2 1.35 13638 729 98.62 0.1712 0.1687 0.1708 0.2145 0.2133 19.58
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 6.7057 f_angle_d 0.7931 f_chiral_restr 0.0506 f_bond_d 0.0058 f_plane_restr 0.0057
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1427 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling REFMAC phasing