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Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-lysine and cladosporin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ELN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 CrpaA.00612.a.A3.PW37710 at 35 mg/ml, protein was incubated with 3 mM MgCl2, L-lysine, and AMPPNP, then mixed 1:1 with Index(g5): 25% (w/v) PEG-3350, 0.2 M lithium sulfate, 0.1 M Tris base/ HCl, pH = 8.5. Crystals were then soaked in a solution that was the previous crystallizaiton condition suplemented with 3 mM lysine and 2 mM cladopsorin for 24 hours, then cryoprotected with 20% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.58 52.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.22 α = 90 b = 120.72 β = 90.23 c = 143.33 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 CCD MARMOSAIC 225 mm CCD Beryllium Lenses 2015-08-07 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 1.9 50 99.6 0.091 10.98 4.1 194875 -3 20.97
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 1.9 1.95 99.9 0.512 2.84 4.2
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 5ELN 1.9 47.07 1.35 194872 1994 99.6 0.204 0.204 0.2038 0.246 0.2466 30.01
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 14.755 f_angle_d 1.066 f_chiral_restr 0.06 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15928 Nucleic Acid Atoms Solvent Atoms 1969 Heterogen Atoms 158
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction