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- PDB-8pjy: Crystal structure of the computationally designed SAKe6EEref protein -
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Open data
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Basic information
Entry | Database: PDB / ID: 8pjy | ||||||||||||
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Title | Crystal structure of the computationally designed SAKe6EEref protein | ||||||||||||
![]() | SAKe6EEref | ||||||||||||
![]() | UNKNOWN FUNCTION / computational / design / scaffold / propeller / Kelch | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Wouters, S.M.L. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Computational design of the SAKe scaffold proteins Authors: Wouters, S.M.L. / Noguchi, H. / Voet, A.R.D. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 174.1 KB | Display | ![]() |
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PDB format | ![]() | 134.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.8 KB | Display | ![]() |
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Full document | ![]() | 424 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 23.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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: 31005.018 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.12 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion Details: 0.2 M Ammonium acetate, 0.1 M bis-Tris pH 5.5, 25 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→42.76 Å / Num. obs: 64797 / % possible obs: 99.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 13.52 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.02 / Rrim(I) all: 0.044 / Net I/σ(I): 18.4 / Num. measured all: 300926 |
Reflection shell | Resolution: 1.3→1.32 Å / % possible obs: 99.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.645 / Num. measured all: 15047 / Num. unique obs: 3261 / CC1/2: 0.835 / Rpim(I) all: 0.332 / Rrim(I) all: 0.728 / Net I/σ(I) obs: 2.3 |
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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: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→42.76 Å
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Refine LS restraints |
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LS refinement shell |
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