☰ Navigation Tabs
Crystal structure of the Norovirus GII.4 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 28NP Dimer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2M NaSCN 24% PEG3350
Cryo: 30% PEG3350. 20mM ligand
Crystal Properties Matthews coefficient Solvent content 2.09 41.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.581 α = 90 b = 128.198 β = 93.078 c = 102.701 γ = 90
Symmetry Space Group I 1 2 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 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) 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 2 46.62 99.9 0.096 0.117 0.066 0.99 10.4 6 75252 28.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.04 0.621 0.753 0.422 0.79
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 46.618 75249 3857 99.846 0.182 0.1791 0.1881 0.233 0.2369 29.6
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] 0.07 1.442 -0.953 0.723
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.53 r_dihedral_angle_2_deg 12.694 r_dihedral_angle_3_deg 12.154 r_dihedral_angle_1_deg 7.327 r_lrange_it 5.872 r_lrange_other 5.856 r_scangle_it 4.195 r_scangle_other 4.186 r_mcangle_it 3.441 r_mcangle_other 3.441
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.53 r_dihedral_angle_2_deg 12.694 r_dihedral_angle_3_deg 12.154 r_dihedral_angle_1_deg 7.327 r_lrange_it 5.872 r_lrange_other 5.856 r_scangle_it 4.195 r_scangle_other 4.186 r_mcangle_it 3.441 r_mcangle_other 3.441 r_scbond_it 2.731 r_scbond_other 2.716 r_mcbond_it 2.386 r_mcbond_other 2.386 r_angle_refined_deg 1.432 r_angle_other_deg 0.5 r_symmetry_nbd_refined 0.242 r_nbd_other 0.241 r_nbd_refined 0.237 r_symmetry_nbd_other 0.207 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.169 r_xyhbond_nbd_refined 0.147 r_metal_ion_refined 0.113 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.071 r_symmetry_xyhbond_nbd_other 0.026 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9516 Nucleic Acid Atoms Solvent Atoms 519 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing