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GII.22 human norovirus protruding domain in complex with glycochenodeoxycholate (GCDCA)
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 0.2 M Ammonium acetate
0.1 M Sodium acetate pH 4.6
30%(w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.16 61.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.24 α = 90 b = 81.24 β = 90 c = 223.91 γ = 120
Symmetry Space Group P 65 2 2
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 PILATUS 6M-F 2017-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.072270 ESRF ID29
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 1.54 59.86 99.36 0.05719 0.05943 0.01599 0.999 27.7 13.7 44206 16.68
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 1.54 1.59 94.22 0.6674 0.694 0.1883 0.938 3.57 13.3
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 2.295 43.804 1.38 20419 1022 99.86 0.177 0.175 0.1787 0.2137 0.2163
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 10.803 f_angle_d 0.588 f_chiral_restr 0.048 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2328 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing