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Crystal structure of Mycobacterium tuberculosis phenylalanyl-tRNA synthetase in complex with compound GDI05-001
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DAW
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 = 268.38 α = 90 b = 298.801 β = 90 c = 65.712 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 2019-01-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97849 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 2.71 50 99.9 0.133 0.985 10.42 6.9 72740 45.3
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 2.71 2.75 100 0.766 0.851 3.26 6.2
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 7DAW 2.71 42.16 1.33 63924 3209 87.78 0.1942 0.1929 0.1941 0.2189 0.2177 43.54
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 21.7808 f_angle_d 1.0965 f_chiral_restr 0.0607 f_bond_d 0.0093 f_plane_restr 0.0082
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8346 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 90
Software Software Software Name Purpose PHENIX refinement PHENIX phasing Coot model building HKL-2000 data reduction HKL-2000 data scaling