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Crystal structure of the Norovirus GII.17 P domain in complex with Difucosyllactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 28WR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2M Mg Sulfate, 16% PEG3350, 0.1 M TRIS pH 8.5
Cryo: 30% PEG3350. 20mM ligand
Crystal Properties Matthews coefficient Solvent content 2.32 46.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.407 α = 90 b = 86.161 β = 106.189 c = 64.056 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER X 16M 2025-02-14 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 1.43 42.74 99.7 0.046 0.055 0.029 0.99 20.1 6.7 113608 10.7
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 1.43 1.46 0.323 0.389 0.214 0.95
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 1.431 42.54 113579 5767 99.651 0.131 0.13 0.13 0.1594 0.1593 14.377
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] 0.167 -0.072 0.277 -0.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.529 r_lrange_it 15.657 r_lrange_other 12.743 r_dihedral_angle_2_deg 10.732 r_dihedral_angle_3_deg 10.555 r_scangle_it 8.068 r_scangle_other 8.067 r_dihedral_angle_1_deg 7.127 r_mcangle_it 6.453 r_mcangle_other 6.452
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.529 r_lrange_it 15.657 r_lrange_other 12.743 r_dihedral_angle_2_deg 10.732 r_dihedral_angle_3_deg 10.555 r_scangle_it 8.068 r_scangle_other 8.067 r_dihedral_angle_1_deg 7.127 r_mcangle_it 6.453 r_mcangle_other 6.452 r_scbond_it 5.62 r_scbond_other 5.619 r_mcbond_it 4.394 r_mcbond_other 4.394 r_rigid_bond_restr 3.49 r_angle_refined_deg 1.575 r_angle_other_deg 0.577 r_nbd_refined 0.266 r_nbd_other 0.219 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.181 r_symmetry_nbd_refined 0.169 r_xyhbond_nbd_refined 0.148 r_symmetry_xyhbond_nbd_refined 0.138 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4775 Nucleic Acid Atoms Solvent Atoms 1012 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing