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Crystal structure of the Norovirus GII.4 P domain in complex with 3 sialyl fucosyllactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OOV Dimer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2M NaSCN 24% PEG3350
Cryo: 30% PEG3350. 20mM ligand
Crystal Properties Matthews coefficient Solvent content 2.09 41.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.917 α = 90 b = 100.231 β = 90 c = 130.475 γ = 90
Symmetry Space Group I 2 2 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 PIXEL DECTRIS EIGER X 16M 2024-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97856 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.95 46.28 100 0.104 0.118 0.039 0.998 12.8 8.7 41854 18.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 99.9 0.64 0.725 0.24 0.826 3.1 8.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.95 46.28 41852 2079 99.959 0.147 0.1442 0.1566 0.1997 0.2078 22.236
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] -0.177 -0.388 0.565
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.262 r_dihedral_angle_2_deg 13.852 r_dihedral_angle_3_deg 12.653 r_lrange_it 7.411 r_lrange_other 7.324 r_dihedral_angle_1_deg 7.036 r_scangle_it 6.346 r_scangle_other 6.345 r_scbond_it 4.922 r_scbond_other 4.921
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.262 r_dihedral_angle_2_deg 13.852 r_dihedral_angle_3_deg 12.653 r_lrange_it 7.411 r_lrange_other 7.324 r_dihedral_angle_1_deg 7.036 r_scangle_it 6.346 r_scangle_other 6.345 r_scbond_it 4.922 r_scbond_other 4.921 r_mcangle_other 4.392 r_mcangle_it 4.391 r_mcbond_it 3.53 r_mcbond_other 3.519 r_angle_refined_deg 2.106 r_angle_other_deg 0.754 r_symmetry_nbd_refined 0.279 r_nbd_other 0.257 r_nbd_refined 0.241 r_symmetry_nbd_other 0.212 r_metal_ion_refined 0.193 r_symmetry_xyhbond_nbd_refined 0.19 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.119 r_symmetry_nbtor_other 0.089 r_bond_refined_d 0.018 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4800 Nucleic Acid Atoms Solvent Atoms 616 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing