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Structure of GII.4 norovirus in complex with Nanobody 30
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X7E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 (0.2 M calcium chloride and 20% [w/v] PEG3350)
Crystal Properties Matthews coefficient Solvent content 2.24 45.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.767 α = 90 b = 62.443 β = 101.24 c = 121.396 γ = 90
Symmetry Space Group I 1 2 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 PILATUS 6M-F 2019-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID13 0.97626 ESRF ID13
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 2.4 57.75 99.8 0.167 0.187 0.082 0.977 5.5 5 34103 27.7
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 2.4 2.49 98.7 0.554 0.629 0.292 0.748 4.6
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 THROUGHOUT 4X7E 2.4 57.75 1.34 34056 3844 98.88 0.2099 0.2066 0.2063 0.2635 0.2635 28.3294
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6890 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing