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Crystal structure of Mycobacterium tuberculosis phenylalanyl-tRNA synthetase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PCO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 1.1M (NH4)2SO4, 0.2% PEG 3350, 0.1M HEPES pH 7.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 267 α = 90 b = 298.91 β = 90 c = 65.936 γ = 90
Symmetry Space Group C 2 2 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 2018-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97886 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.83 50 93.5 0.174 0.964 10.86 2.7 59426 59.32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.83 2.87 71.5 0.455 0.84 1.67
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 3PCO 2.83 49.82 1.36 59346 2984 93.1 0.2019 0.1999 0.2021 0.2396 0.2393 61.02
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 23.3067 f_angle_d 1.1032 f_chiral_restr 0.0626 f_bond_d 0.0091 f_plane_restr 0.0077
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8336 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 60
Software Software Software Name Purpose PHENIX refinement PHENIX phasing HKL-2000 data reduction HKL-2000 data scaling Coot model building