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Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium ulcerans complexed with L-lysine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A74
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 MyulA.00612.a.B1.PW37993 at 28 mg/ml was incubated with 3 mM MgCl2, AMPPNP, and L-Lysine, then mixed 1:1 with Morpheus(e9): 10% (w/v) PEG-20,000, 20% (v/v) PEG MME 550, 0.1 M bicine/ Trisma base, pH = 8.5, and 0.03 M each diethyleneglycol, triethyleneglycol, tetraethyleneglycol, pentaethylene glycol
Crystal Properties Matthews coefficient Solvent content 3.65 66.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.04 α = 90.38 b = 96.69 β = 104.84 c = 105.56 γ = 117.15
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 2017-04-12 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 2.7 46.455 98.8 0.082 0.096 0.997 12.14 3.945 86858 -3 52.3
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 2.7 2.77 98.2 0.599 0.692 0.805 2.36 3.986
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 3A74 2.7 46.455 1.98 86835 2193 98.86 0.1777 0.177 0.1807 0.2043 0.2076 63.6092
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 16.497 f_angle_d 0.5 f_chiral_restr 0.04 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14866 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 101
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction MoRDa phasing