+
Open data
-
Basic information
Entry | Database: PDB / ID: 8dah | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | [20 bp edge] Self-Assembled 3D DNA Hexagonal Tensegrity Triangle | ||||||||||||||||||||||||
![]() |
| ||||||||||||||||||||||||
![]() | 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 | ![]()
| ||||||||||||||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 64.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 41 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 372.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 374.1 KB | Display | |
Data in XML | ![]() | 2.6 KB | Display | |
Data in CIF | ![]() | 3.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8cs1C ![]() 8cs2C ![]() 8cs3C ![]() 8cs4C ![]() 8cs5C ![]() 8cs6C ![]() 8cs7C ![]() 8cs8C ![]() 8cymC ![]() 8cynC ![]() 8dagC ![]() 8dcjC ![]() 7r96S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
Unit cell |
|
-
Components
#1: DNA chain | Mass: 6143.981 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#2: DNA chain | Mass: 2082.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 1825.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 2128.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 10.26 Å3/Da / Density % sol: 88.01 % |
---|---|
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 |
---|---|
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: 5.47→61.3 Å / Num. obs: 1396 / % possible obs: 88.5 % / Redundancy: 13.7 % / Biso Wilson estimate: 334.89 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 5.47→6.12 Å / Num. unique obs: 203 / CC1/2: 0.482 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 7R96 Resolution: 5.47→40.13 Å / SU ML: 0.3046 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.0699 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 356.38 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 5.47→40.13 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 5.47→40.13 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -47.8625461798 Å / Origin y: 27.9697166215 Å / Origin z: 14.953053516 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |