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Crystal structure of the Norovirus GII.4 P domain in complex with Lacto-N-fucopentaose III (LNFP III)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 28NP Dimer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 m NaSCN 24% PEG3350
Cryo: 30% PEG3350 20mM ligand
Crystal Properties Matthews coefficient Solvent content 2.13 42.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.293 α = 90 b = 102.041 β = 90 c = 130.335 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) 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 2.6 46.49 97.2 0.162 0.078 0.993 9.6 8.8 17655 36.8
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 2.6 2.72 98.9 0.737 0.825 0.361 0.732 2.7 8.8
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 2.6 41.765 17654 907 96.56 0.194 0.1897 0.1958 0.2654 0.2632 37.531
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] -0.214 -0.033 0.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.155 r_dihedral_angle_3_deg 14.853 r_dihedral_angle_2_deg 7.9 r_dihedral_angle_1_deg 6.901 r_lrange_it 6.343 r_lrange_other 6.343 r_mcangle_it 4.306 r_mcangle_other 4.306 r_scangle_it 4.271 r_scangle_other 4.271
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.155 r_dihedral_angle_3_deg 14.853 r_dihedral_angle_2_deg 7.9 r_dihedral_angle_1_deg 6.901 r_lrange_it 6.343 r_lrange_other 6.343 r_mcangle_it 4.306 r_mcangle_other 4.306 r_scangle_it 4.271 r_scangle_other 4.271 r_mcbond_it 2.715 r_mcbond_other 2.715 r_scbond_it 2.698 r_scbond_other 2.697 r_angle_refined_deg 1.308 r_angle_other_deg 0.477 r_symmetry_nbd_other 0.247 r_nbd_other 0.206 r_nbd_refined 0.189 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.151 r_xyhbond_nbd_refined 0.138 r_symmetry_xyhbond_nbd_refined 0.11 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.061 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4764 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing