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Crystal structure of the carbohydrate-binding domain VP8* of human P[4] rotavirus strain BM5265 in complex with LNDFH I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UT9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 298 0.2 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate pH 4.6, 25% w/v Polyethylene glycol 4,000
Crystal Properties Matthews coefficient Solvent content 2.09 41.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.319 α = 104.73 b = 38.432 β = 90.11 c = 55.808 γ = 96.04
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 2020-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97932 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 2.54 53.95 98.8 0.195 0.221 0.084 0.979 5.9 6.6 9452
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 2.54 2.58 99.8 0.455 0.523 0.206 0.84 1.7 6.3
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 6UT9 2.54 53.95 8970 482 98.8 0.2077 0.2048 0.2091 0.2608 0.2621 RANDOM 25.953
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 2.41 0.52 1.68 0.78 -2.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.749 r_dihedral_angle_3_deg 16.477 r_dihedral_angle_4_deg 14.81 r_dihedral_angle_1_deg 8.26 r_angle_refined_deg 1.689 r_angle_other_deg 1.224 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.749 r_dihedral_angle_3_deg 16.477 r_dihedral_angle_4_deg 14.81 r_dihedral_angle_1_deg 8.26 r_angle_refined_deg 1.689 r_angle_other_deg 1.224 r_chiral_restr 0.074 r_bond_refined_d 0.009 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 2567 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction DIALS data reduction PHASER phasing