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Three viral endonucleases bound to the same inhibitor (9-hydroxy-3,4-dihydro-2H-pyrazino[1,2-c]pyrimidine-1,8-dione derivative). (2) La Crosse virus L protein endonuclease with manganese ions.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XI7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 288 0.20 M Ammonium sulphate
0.1 M bis-Tris pH6
20 % PEG 3350
Cryo: 20 % glycerol
Crystal Properties Matthews coefficient Solvent content 3.24 62.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.79 α = 90 b = 103.36 β = 90 c = 105.24 γ = 90
Symmetry Space Group I 21 21 21
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 MAR CCD 300 mm 2013-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
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 2.8 50 99 0.118 0.155 0.984 7.39 2.3 13326 40.84
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 2.8 2.87 99.6 0.659 0.863 0.572 1.39
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.8 36.87 1 13326 604 99 0.1867 0.1847 0.1862 0.2261 0.2293 40.28
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 13.3876 f_angle_d 0.5695 f_chiral_restr 0.0451 f_plane_restr 0.0044 f_bond_d 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 51
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing