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- PDB-8dag: [8 bp center] Self-Assembled 3D DNA Hexagonal Tensegrity Triangle -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dag | ||||||||||||||||||||||||
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Title | [8 bp center] Self-Assembled 3D DNA Hexagonal Tensegrity Triangle | ||||||||||||||||||||||||
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![]() | DNA / tensegrity triangle / synthetic construct / self-assembly | ||||||||||||||||||||||||
Function / homology | DNA / DNA (> 10)![]() | ||||||||||||||||||||||||
Biological species | synthetic construct (others) | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Lu, B. / Vecchioni, S. / Ohayon, Y.P. / Seeman, N.C. / Mao, C. / Sha, R. | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Programmable 3D Hexagonal Geometry of DNA Tensegrity Triangles. Authors: Lu, B. / Woloszyn, K. / Ohayon, Y.P. / Yang, B. / Zhang, C. / Mao, C. / Seeman, N.C. / Vecchioni, S. / 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 | ![]() | 67.8 KB | Display | ![]() |
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PDB format | ![]() | 43.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 373.6 KB | Display | ![]() |
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Full document | ![]() | 382 KB | Display | |
Data in XML | ![]() | 3.6 KB | Display | |
Data in CIF | ![]() | 4.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8cs1C ![]() 8cs2C ![]() 8cs3C ![]() 8cs4C ![]() 8cs5C ![]() 8cs6C ![]() 8cs7C ![]() 8cs8C ![]() 8cymC ![]() 8cynC ![]() 8dahC ![]() 8dcjC ![]() 7r96S 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: 6497.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 2371.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 1496.011 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 2432.614 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: 10.25 Å3/Da / Density % sol: 88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 1.75 M ammonium sulfate, 120 mM Tris, 120 mM Acetic Acid, 6 mM EDTA Temp details: 338-293 at 0.4/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: Jun 12, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00743 Å / Relative weight: 1 |
Reflection | Resolution: 6.16→65.21 Å / Num. obs: 1054 / % possible obs: 89.3 % / Redundancy: 19.8 % / Biso Wilson estimate: 500.14 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 6.16→7.02 Å / Num. unique obs: 211 / CC1/2: 0.344 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7R96 Resolution: 6.16→42.69 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.0171 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: 684.79 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 6.16→42.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 6.16→42.69 Å
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Refinement TLS params. | Method: refined / Origin x: 50.3302978637 Å / Origin y: -29.7575317618 Å / Origin z: 10.4001421056 Å
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Refinement TLS group | Selection details: all |