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Crystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and fragment DDD00805735
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KA0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 ammonium acetate
HEPES pH 7.5
PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.88 57.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.773 α = 90 b = 65.25 β = 109.736 c = 191.846 γ = 90
Symmetry Space Group P 1 21 1
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 S 6M 2019-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97937 APS 19-ID
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 2.51 50 98.4 0.092 0.1 0.038 0.996 8.3 6.6 117034
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 2.51 2.55 98.3 1.04 1.127 0.429 0.744 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.51 48.42 1.34 110669 5475 92.87 0.2088 0.2071 0.207 0.2406 0.2398 55.56
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 22.1713 f_angle_d 0.4256 f_chiral_restr 0.0376 f_plane_restr 0.0042 f_bond_d 0.0016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17531 Nucleic Acid Atoms 3169 Solvent Atoms 999 Heterogen Atoms 164
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction SCALEPACK data scaling MOLREP phasing