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Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium thermoresistibile complexed with L-lysine and Cladosporin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VL1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.1 290 MythA.00612.a.B1.PW38257 at 33.5 mg/ml was incubated with 2 mM L-Lysine and 1 mM cladosporin, then mixed 1:1 with MCSG1 (d12): 0.2 M ammonium chloride, pH = 6.3, 20% (w/v) PEG-3350, cryoprotected with 20% ethylene glycol. Tray: 293203d12, puck: ryc9-9.
Crystal Properties Matthews coefficient Solvent content 2.5 50.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.46 α = 93.34 b = 88.16 β = 96.45 c = 123.43 γ = 98.93
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 300 mm CCD Beryllium Lenses 2017-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.35 42.457 94.8 0.054 0.072 0.997 10.13 2.285 87176 -3 47.06
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.41 95.5 0.576 0.751 0.866 1.97 2.378
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5VL1 2.35 42.457 1.98 86921 2073 94.58 0.225 0.2243 0.2538 0.2852 59.27
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 14.724 f_angle_d 0.437 f_chiral_restr 0.04 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14952 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 132
Software Software Software Name Purpose XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction