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Open data
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Basic information
Entry | Database: PDB / ID: 8y6c | ||||||
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Title | Norovirus GII.10 P domain and 2'-FL (powder) | ||||||
![]() | GII.10 norovirus P domain in complex with 2'FL (powder) | ||||||
![]() | VIRAL PROTEIN / Sugar / complex / milk oligosaccharide | ||||||
Function / homology | DI(HYDROXYETHYL)ETHER![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hansman, G. / Tame, J.R.H. / Kher, G. / Pancera, M. | ||||||
Funding support | 1items
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![]() | ![]() Title: Norovirus GII.10 P domain and 2'-FL (powder) Authors: Hansman, G. / Tame, J.R.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 254.7 KB | Display | ![]() |
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PDB format | ![]() | 204.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 32.8 KB | Display | |
Data in CIF | ![]() | 49.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34506.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: THE GENEBANK ACCESSION NUMBER IS AF504671 FOR THIS PROTEIN. Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54.02 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop Details: 0.2 M sodium nitrate 0.1 M bis-tris propane (pH 7.5) 20% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95365 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→44.63 Å / Num. obs: 122545 / % possible obs: 99 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.035 / Rrim(I) all: 0.075 / Χ2: 0.51 / Net I/σ(I): 9.2 / Num. measured all: 556487 |
Reflection shell | Resolution: 1.47→1.49 Å / % possible obs: 84.1 % / Redundancy: 4.3 % / Rmerge(I) obs: 1.313 / Num. measured all: 21864 / Num. unique obs: 5094 / CC1/2: 0.395 / Rpim(I) all: 0.702 / Rrim(I) all: 1.494 / Χ2: 0.41 / Net I/σ(I) obs: 0.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.47→44.63 Å
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Refine LS restraints |
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LS refinement shell |
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