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- PDB-8sjr: [3T17] Self-assembling right-handed tensegrity triangle with 17 i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8sjr | |||||||||||||||||||||
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Title | [3T17] Self-assembling right-handed tensegrity triangle with 17 interjunction base pairs and R3 symmetry | |||||||||||||||||||||
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![]() | DNA / Tensegrity triangle / DNA nanotechnology / nanomaterials | |||||||||||||||||||||
Function / homology | DNA / DNA (> 10)![]() | |||||||||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Janowski, J. / Vecchioni, S. / Sha, R. / Ohayon, Y.P. | |||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Engineering tertiary chirality in helical biopolymers. Authors: Janowski, J. / Pham, V.A.B. / Vecchioni, S. / Woloszyn, K. / Lu, B. / Zou, Y. / Erkalo, B. / Perren, L. / Rueb, J. / Madnick, J. / Mao, C. / Saito, M. / Ohayon, Y.P. / Jonoska, N. / Sha, R. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.6 KB | Display | ![]() |
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PDB format | ![]() | 60.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 372.6 KB | Display | ![]() |
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Full document | ![]() | 376.1 KB | Display | |
Data in XML | ![]() | 3 KB | Display | |
Data in CIF | ![]() | 3.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8sjmC ![]() 8sjnC ![]() 8sjoC ![]() 8sjpC ![]() 8sjqC ![]() 8sjsC ![]() 8sjtC ![]() 8sjuC ![]() 8sjvC ![]() 8sjwC ![]() 8sl5C ![]() 8sz5C ![]() 5w6wS S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components
#1: DNA chain | Mass: 5783.765 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 5187.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 4303.775 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 3703.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 11.79 Å3/Da / Density % sol: 89.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 100 mM MOPS, 1.25 M magnesium sulfate / Temp details: 338K-293K at 0.4K/hr |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 21, 2021 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1.00744 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 5.25→85.107 Å / Num. obs: 3630 / % possible obs: 81 % / Redundancy: 9.7 % / Biso Wilson estimate: 412.28 Å2 / CC1/2: 0.903 / Net I/σ(I): 6.7 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5W6W Resolution: 5.25→38.72 Å / SU ML: -0 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 48.7139 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: 407.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 5.25→38.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 5.25→38.72 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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