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VP8* domain of the spike protein VP4 from bovine P[3] strain of rotavirus species C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294 Sodium Acetate 1.5 M pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.025 39.31292
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.489 α = 90 b = 64.37 β = 90 c = 76.937 γ = 90
Symmetry Space Group P 21 21 21
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 2023-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97918 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 3 76.94 99.9 0.365 0.379 0.104 0.986 7.7 12.9 6504
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 3 3.18 99.7 1.084 1.126 0.303 0.873 13.5
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3 49.37 6152 322 99.77 0.24714 0.24438 0.29722 0.2666 RANDOM 34.166
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] -4.27 1.7 2.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.861 r_dihedral_angle_1_deg 5.85 r_long_range_B_refined 1.741 r_long_range_B_other 1.738 r_dihedral_angle_2_deg 1.618 r_mcangle_it 0.684 r_mcangle_other 0.684 r_angle_refined_deg 0.578 r_scangle_other 0.384 r_mcbond_it 0.362
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.861 r_dihedral_angle_1_deg 5.85 r_long_range_B_refined 1.741 r_long_range_B_other 1.738 r_dihedral_angle_2_deg 1.618 r_mcangle_it 0.684 r_mcangle_other 0.684 r_angle_refined_deg 0.578 r_scangle_other 0.384 r_mcbond_it 0.362 r_mcbond_other 0.362 r_angle_other_deg 0.221 r_scbond_it 0.183 r_scbond_other 0.183 r_chiral_restr 0.027 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2572 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing