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GII.10 human norovirus protruding domain in complex with taurochenodeoxycholate (TCDCA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ONU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0,1M Magnesium acetate tetrahydrate
0,1M Sodium citrate pH 5,8
14% w/v PEG 5000 MME
Crystal Properties Matthews coefficient Solvent content 2.76 55.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.83 α = 90 b = 87.91 β = 90 c = 108.34 γ = 90
Symmetry Space Group P 21 2 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 PILATUS3 6M 2017-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.973720 ESRF ID30B
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 2.05 46.12 99.65 0.09804 0.107 0.04248 0.997 11.02 6.3 48586 34.59
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 2.05 2.12 97.33 0.6477 0.7062 0.2783 0.793 2.26 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3ONU 2.05 46.118 1.38 48564 2430 99.66 0.1713 0.1695 0.1706 0.2063 0.207
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.018 f_angle_d 0.685 f_chiral_restr 0.049 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4694 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 88
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing