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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 25%PEG 6000
0.1M Na-HEPES pH7.5
0.1M LiCl
Crystal Properties Matthews coefficient Solvent content 1.92 35.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.739 α = 90 b = 54.641 β = 97.73 c = 67.944 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 0.97928 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 1.85 67.33 99.2 0.088 0.103 0.053 0.997 9.5 3.6 23811
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 1.85 1.95 98.9 0.699 0.824 0.431 0.746 3.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6H9W 1.85 67.33 22633 1162 99.09 0.1788 0.1761 0.2328 0.237 RANDOM 25.359
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] 1.58 -1.74 -2.53 1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.284 r_dihedral_angle_3_deg 13.853 r_dihedral_angle_4_deg 11.606 r_dihedral_angle_1_deg 6.841 r_angle_refined_deg 1.718 r_angle_other_deg 1.001 r_chiral_restr 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.284 r_dihedral_angle_3_deg 13.853 r_dihedral_angle_4_deg 11.606 r_dihedral_angle_1_deg 6.841 r_angle_refined_deg 1.718 r_angle_other_deg 1.001 r_chiral_restr 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2604 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 36
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing