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Crystal Structure of Lysyl-tRNA synthetase from Stenotrophomonas maltophilia with bound L-lysine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BBU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 287 StmaA.00612.a.B1.PW38745 at 10 mg/ml was incubated with 2 mM L-lysine and adenosine, then mixed 1:1 with Morpheus(H6): 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.1 M MOPS/HEPES-Na pH 7.5, 0.02 M each sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine. Tray 313975h6. Puck xdi4-1.
Crystal Properties Matthews coefficient Solvent content 3.19 61.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.16 α = 90 b = 127.16 β = 90 c = 158.7 γ = 120
Symmetry Space Group P 31 2 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 CCD RAYONIX MX-300 Beryllium Lenses 2020-02-13 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 2.05 50 93.3 0.08 0.085 0.999 17.32 8.035 87130 35.416
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 2.05 2.1 95.6 0.56 0.6 0.878 3.4 7.897
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1BBU 2.05 41.62 83260 4958 89.25 0.1514 0.1494 0.1507 0.1839 0.1858 37.26
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 16.7947 f_angle_d 0.8054 f_chiral_restr 0.0507 f_bond_d 0.0072 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7503 Nucleic Acid Atoms Solvent Atoms 548 Heterogen Atoms 222
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MoRDa phasing