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Crystal structure of the Norovirus GII.17 P domain in complex with Lacto-N-fucopentaose I (LNFP I)
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 2.35 47.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.225 α = 90 b = 85.512 β = 106.232 c = 65.623 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 2025-10-02 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 1.71 47.395 95.6 0.052 0.063 0.052 0.99 6.9 3.5 64492
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 1.71 1.74 47.4 0.524 0.689 0.443 0.64
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 1.713 47.395 64465 3183 95.555 0.168 0.1659 0.1776 0.2024 0.2126 17.77
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] -0.719 -0.322 -1.187 1.791
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.121 r_dihedral_angle_3_deg 11.049 r_dihedral_angle_2_deg 9.765 r_dihedral_angle_1_deg 7.51 r_lrange_it 5.252 r_lrange_other 5.018 r_scangle_it 3.623 r_scangle_other 3.623 r_mcangle_it 2.449 r_mcangle_other 2.449
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.121 r_dihedral_angle_3_deg 11.049 r_dihedral_angle_2_deg 9.765 r_dihedral_angle_1_deg 7.51 r_lrange_it 5.252 r_lrange_other 5.018 r_scangle_it 3.623 r_scangle_other 3.623 r_mcangle_it 2.449 r_mcangle_other 2.449 r_scbond_it 2.386 r_scbond_other 2.386 r_mcbond_it 1.657 r_mcbond_other 1.657 r_angle_refined_deg 1.551 r_angle_other_deg 0.573 r_symmetry_nbd_other 0.238 r_symmetry_xyhbond_nbd_refined 0.201 r_nbd_refined 0.195 r_nbtor_refined 0.18 r_nbd_other 0.168 r_symmetry_nbd_refined 0.166 r_xyhbond_nbd_refined 0.144 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.083 r_xyhbond_nbd_other 0.052 r_symmetry_xyhbond_nbd_other 0.031 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4766 Nucleic Acid Atoms Solvent Atoms 912 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing