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Unraveling the role of the secretor antigen in human rotavirus attachment to histo-blood group antigens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H9W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294.15 1.5M Li2SO4
0.1M Tris pH6.5
Crystal Properties Matthews coefficient Solvent content 1.92 35.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.988 α = 90 b = 54.725 β = 97.92 c = 67.433 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 PILATUS 6M 2017-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97907 ALBA XALOC
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 1.31 66.79 94.9 0.087 0.102 0.053 0.995 8.4 3.4 64030
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 1.31 1.38 97.6 0.6 0.736 0.419 0.739 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6H9W 1.31 66.79 60807 3204 94.76 0.1821 0.1806 0.1801 0.209 0.2084 RANDOM 12.386
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] 0.35 -0.42 -0.29 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.796 r_dihedral_angle_4_deg 17.353 r_dihedral_angle_3_deg 13.159 r_dihedral_angle_1_deg 6.26 r_angle_other_deg 3.817 r_angle_refined_deg 2.106 r_chiral_restr 0.155 r_gen_planes_other 0.032 r_bond_refined_d 0.023 r_gen_planes_refined 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.796 r_dihedral_angle_4_deg 17.353 r_dihedral_angle_3_deg 13.159 r_dihedral_angle_1_deg 6.26 r_angle_other_deg 3.817 r_angle_refined_deg 2.106 r_chiral_restr 0.155 r_gen_planes_other 0.032 r_bond_refined_d 0.023 r_gen_planes_refined 0.014 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2610 Nucleic Acid Atoms Solvent Atoms 512 Heterogen Atoms 40
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing