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Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-lysine and Adenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ELO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.89 290 CrpaA.00612.a.A3.PW37710 at 35 mg/ml, protein was incubated with 4 mM L-lysine and 4 mM Adenosine, then mixed 1:1 with 26.14% (w/v) PEG-3350, 0.2 M lithium sulfate, 0.1 M Tris-HCl/NaOH, pH = 7.89. Crystals were cryoprotected with 20% ethylene glycol. Puck: pqf5-7, tray: 296117b9.
Crystal Properties Matthews coefficient Solvent content 2.49 50.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.87 α = 90 b = 142.63 β = 90 c = 72.91 γ = 90
Symmetry Space Group P 21 21 2
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 2017-11-02 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) 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 1.85 46.792 99.7 0.062 18 4.977 105099 -3 21.84
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.9 100 0.598 2.88 4.99
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 5ELO 1.85 46.79 1.34 105085 1947 99.7 0.153 0.152 0.1526 0.185 0.1858 29.86
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8003 Nucleic Acid Atoms Solvent Atoms 1082 Heterogen Atoms 133
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction