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Crystal Structure of the Murine Norovirus VP1 P domain in complex with the CD300lf Receptor and Lithocholic Acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LQ6 PDB entries 3LQ6 & 5FFL experimental model PDB 5FFL PDB entries 3LQ6 & 5FFL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.7 293 0.1 M Tris, pH 8.7, 40 mM calcium chloride, 5.5% PEG10000
Crystal Properties Matthews coefficient Solvent content 2.95 58.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.091 α = 90 b = 152.891 β = 90 c = 70.037 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 CMOS NOIR-1 2017-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.00004 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.8 63.68 95 0.996 5.92 2 95932
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.87 63 0.324 0.65 1.8
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 THROUGHOUT PDB entries 3LQ6 & 5FFL 1.801 63.674 1.34 95929 2552 94.99 0.1751 0.1743 0.1748 0.2039 0.2041 23.9946
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 12.066 f_angle_d 1.109 f_chiral_restr 0.274 f_bond_d 0.022 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6426 Nucleic Acid Atoms Solvent Atoms 1132 Heterogen Atoms 148
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHENIX phasing