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Crystal structure of the Norovirus GII.17 P domain in complex with Lacto-N-fucopentaose II (LNFP II)
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% PSM, 0.1 M TRIS pH 8.5
Cryo: 30% PSM. 20mM ligand
Crystal Properties Matthews coefficient Solvent content 2.32 47.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.5 α = 90 b = 86.274 β = 106.081 c = 63.969 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 1.53 47.66 99.8 0.052 0.063 0.035 0.99 16.7 6.3 92749 13.5
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 1.53 1.56 0.444 0.537 0.3 0.89 3.3
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 1.533 42.781 92720 4687 99.783 0.161 0.1594 0.173 0.1878 0.1976 16.16
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] 0.105 -0.645 -0.717 0.843
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.203 r_dihedral_angle_3_deg 11.592 r_dihedral_angle_2_deg 10.473 r_dihedral_angle_1_deg 7.42 r_lrange_it 5.284 r_lrange_other 5.113 r_scangle_it 3.831 r_scangle_other 3.83 r_scbond_it 2.678 r_scbond_other 2.677
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.203 r_dihedral_angle_3_deg 11.592 r_dihedral_angle_2_deg 10.473 r_dihedral_angle_1_deg 7.42 r_lrange_it 5.284 r_lrange_other 5.113 r_scangle_it 3.831 r_scangle_other 3.83 r_scbond_it 2.678 r_scbond_other 2.677 r_mcangle_other 2.667 r_mcangle_it 2.666 r_mcbond_it 1.808 r_mcbond_other 1.808 r_angle_refined_deg 1.761 r_angle_other_deg 0.637 r_symmetry_nbd_other 0.216 r_nbd_refined 0.201 r_symmetry_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.181 r_nbd_other 0.163 r_xyhbond_nbd_refined 0.133 r_symmetry_nbd_refined 0.117 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4787 Nucleic Acid Atoms Solvent Atoms 804 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing