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GII.10 Vietnam 026 norovirus protruding domain in complex with Nanobody Nano-42
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ONU 3ONU and 4X4C experimental model PDB 4X4C 3ONU and 4X4C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.2 M potassium iodide, 20% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.62 52.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.93 α = 90 b = 105.36 β = 90 c = 107.75 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 PILATUS3 2M 2016-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8729 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 47.327 99.6 0.09 0.102 0.998 13.08 4.497 68217 -3 28.38
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.12 98.8 0.742 0.838 0.749 2.15 4.646
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 and 4X4C 2 47.327 1.36 68128 3409 99.68 0.182 0.1799 0.1855 0.2215 0.1891
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 12.386 f_angle_d 1.082 f_chiral_restr 0.053 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6399 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 156
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction PHASER phasing