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Open data
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Basic information
Entry | Database: PDB / ID: 8k84 | ||||||
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Title | De novo design protein -N3 | ||||||
![]() | De novo design protein | ||||||
![]() | DE NOVO PROTEIN / De novo design protein | ||||||
Function / homology | DI(HYDROXYETHYL)ETHER![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, S. / Liu, Y. | ||||||
Funding support | 1items
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![]() | ![]() Title: De novo design protein -N3 Authors: Wang, S. / Liu, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.1 KB | Display | ![]() |
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PDB format | ![]() | 60.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.2 KB | Display | ![]() |
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Full document | ![]() | 447.1 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 24.1 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19085.541 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() #2: Chemical | ChemComp-PEG / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.85 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / Details: 0.2M Imidazole malate pH5.5 33% w/v PEG600 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 13, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2→59.82 Å / Num. obs: 21086 / % possible obs: 99.3 % / Redundancy: 3 % / Biso Wilson estimate: 19.05 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2→2.05 Å / Num. unique obs: 1527 / CC1/2: 0.584 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→25.01 Å
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Refine LS restraints |
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LS refinement shell |
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