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Crystal structure of the Norovirus GII.17 P domain in complex with Lacto-N-difucohexaose I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZUS Dimer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M magnesium acetate, 14% PSM, 0.1 M Tris pH 8.5.
Cryo: 30% PSM. 20mM ligand
Crystal Properties Matthews coefficient Solvent content 2.29 46.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.811 α = 90 b = 85.923 β = 105.909 c = 64.213 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 1.1 47.24 99.8 0.055 0.065 0.035 0.99 13.9 6.3 247453 8.4
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 1.1 1.12 99.5 0.831 1.03 0.599 0.77 5.5
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 1.1 42.961 234893 12522 99.8 0.139 0.1381 0.1424 0.1611 0.1625 12.736
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] 0.944 0.787 -1.405 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.577 r_lrange_it 14.758 r_lrange_other 11.626 r_dihedral_angle_2_deg 11.073 r_dihedral_angle_3_deg 10.473 r_scangle_it 7.897 r_scangle_other 7.896 r_dihedral_angle_1_deg 6.987 r_scbond_it 5.689 r_scbond_other 5.688
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.577 r_lrange_it 14.758 r_lrange_other 11.626 r_dihedral_angle_2_deg 11.073 r_dihedral_angle_3_deg 10.473 r_scangle_it 7.897 r_scangle_other 7.896 r_dihedral_angle_1_deg 6.987 r_scbond_it 5.689 r_scbond_other 5.688 r_mcangle_it 5.609 r_mcangle_other 5.609 r_rigid_bond_restr 4.622 r_mcbond_it 4.047 r_mcbond_other 4.047 r_angle_refined_deg 1.697 r_angle_other_deg 0.654 r_symmetry_nbd_other 0.275 r_nbd_refined 0.203 r_nbd_other 0.202 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.144 r_symmetry_xyhbond_nbd_refined 0.135 r_symmetry_nbd_refined 0.126 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.087 r_symmetry_xyhbond_nbd_other 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4786 Nucleic Acid Atoms Solvent Atoms 1049 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing