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2-(4-(1H-tetrazol-5-yl)phenyl)-5-hydroxypyrimidin-4(3H)-one bound to influenza 2009 H1N1 endonuclease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4M5Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.7 298 Crystals are formed by mixing in a 1:1 ratio endonuclease (5 mg/ml) with crystallization buffer containing 200 mM MES, 27% PEG8000, 200 mM ammonium sulfate, 1 mM manganese chloride, 10 mM magnesium acetate, 10 mM taurine, and 50 mM sodium fluoride. Crystals form within a few hours and grow to maximum size in one to two weeks
Crystal Properties Matthews coefficient Solvent content 2.61 52.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.986 α = 90 b = 101.637 β = 90 c = 66.512 γ = 90
Symmetry Space Group C 2 2 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 ADSC QUANTUM 270 2013-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.917 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 22.9 99.31 22.39 3.5 27807 27807
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 1.8 1.83 99.2 0.592 1.83 3
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4M5Q 1.8 22.9 27807 1395 99.31 0.1773 0.1756 0.1836 0.2087 0.2126 Random 5%
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 15.134 f_angle_d 1.28 f_chiral_restr 0.053 f_bond_d 0.012 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1646 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 31
Software Software Software Name Purpose PHENIX refinement