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- PDB-8pju: Crystal structure of the computationally designed SAKe6DEtal protein -
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Open data
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Basic information
Entry | Database: PDB / ID: 8pju | ||||||||||||
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Title | Crystal structure of the computationally designed SAKe6DEtal protein | ||||||||||||
![]() | SAKe6DEtal | ||||||||||||
![]() | 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 | ![]() | 116.9 KB | Display | ![]() |
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PDB format | ![]() | 86.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.5 KB | Display | ![]() |
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Full document | ![]() | 425.3 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 16.6 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 33254.430 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: 1.92 Å3/Da / Density % sol: 36.1 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion Details: 0.2 M Lithium sulfate, 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 EIGER X 16M / Detector: PIXEL / Date: Jun 2, 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: 1.72→46.07 Å / Num. obs: 27630 / % possible obs: 100 % / Redundancy: 10.7 % / Biso Wilson estimate: 20.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.03 / Rrim(I) all: 0.099 / Net I/σ(I): 16 / Num. measured all: 295871 |
Reflection shell | Resolution: 1.72→1.75 Å / % possible obs: 99.8 % / Redundancy: 10.6 % / Rmerge(I) obs: 1.078 / Num. measured all: 15275 / Num. unique obs: 1436 / CC1/2: 0.878 / Rpim(I) all: 0.346 / Rrim(I) all: 1.135 / Net I/σ(I) obs: 2.9 |
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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: 28.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→35.51 Å
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Refine LS restraints |
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LS refinement shell |
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