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Crystal structure of P domain from norovirus GI.9 capsid protein in complex with Lewis b antigen.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VP0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 298 magnesium chloride, Bicine, pH 9.0
Crystal Properties Matthews coefficient Solvent content 4.44 72.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.749 α = 90 b = 76.464 β = 124.2 c = 103.281 γ = 90
Symmetry Space Group C 1 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 IMAGE PLATE RIGAKU RAXIS IV++ 2019-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.4 50 98.2 0.073 0.086 18.9 3.7 45674
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 0.333 0.395
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 7VP0 2.4 41.193 1.35 45659 1995 98.13 0.1663 0.1649 0.1665 0.1956 0.1971
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 7.771 f_angle_d 0.973 f_chiral_restr 0.057 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4738 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms 105
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASES phasing