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Crystal structure of P[6] rotavirus vp8* in complex with LNT
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 7.8 295 0.2 M Potassium sodium tartrate tetrahydrate,0.1 M Sodium citrate tribasic dihydrate pH 5.6,2.0 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.15 42.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.681 α = 90 b = 75.354 β = 91.77 c = 74.411 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 2020-06-19 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 1.52 74.38 96.1 0.055 0.066 0.035 0.998 12.4 3.4 92741
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 1.52 1.6 94.9 0.61 0.725 0.387 0.804 3.4
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 1.52 74.38 87918 4797 95.7 0.1753 0.1741 0.1838 0.1964 0.204 RANDOM 19.943
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] -0.92 0.23 0.88 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.936 r_dihedral_angle_4_deg 14.912 r_dihedral_angle_3_deg 11.772 r_dihedral_angle_1_deg 8.123 r_angle_other_deg 1.283 r_angle_refined_deg 1.233 r_chiral_restr 0.074 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.936 r_dihedral_angle_4_deg 14.912 r_dihedral_angle_3_deg 11.772 r_dihedral_angle_1_deg 8.123 r_angle_other_deg 1.283 r_angle_refined_deg 1.233 r_chiral_restr 0.074 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5172 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing