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Crystal structure of the carbohydrate-binding domain VP8* of human P[4] rotavirus strain BM5265
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NIW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 298 0.1 M BIS-TRIS pH 5.5,
25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.12 42.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.04 α = 90 b = 32.448 β = 94.64 c = 50.997 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 PILATUS3 S 6M 2019-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
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 1.21 50.83 95.1 0.053 0.063 0.034 0.998 10.5 3.3 44980
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 1.21 1.27 97.6 0.434 0.521 0.282 0.85 3.3
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 6NIW 1.21 50.83 42612 2356 94.77 0.1886 0.1873 0.1899 0.2113 0.2105 RANDOM 11.746
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] 0.78 -0.56 -0.34 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.572 r_dihedral_angle_4_deg 15.205 r_dihedral_angle_3_deg 11.316 r_dihedral_angle_1_deg 8.326 r_angle_refined_deg 1.47 r_angle_other_deg 1.398 r_chiral_restr 0.084 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.572 r_dihedral_angle_4_deg 15.205 r_dihedral_angle_3_deg 11.316 r_dihedral_angle_1_deg 8.326 r_angle_refined_deg 1.47 r_angle_other_deg 1.398 r_chiral_restr 0.084 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1297 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing