+Open data
-Basic information
Entry | Database: PDB / ID: 8dah | ||||||||||||||||||||||||
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Title | [20 bp edge] Self-Assembled 3D DNA Hexagonal Tensegrity Triangle | ||||||||||||||||||||||||
Components |
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Keywords | DNA / tensegrity triangle / synthetic construct / self-assembly | ||||||||||||||||||||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||||||||||||||||||||
Biological species | synthetic construct (others) | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.47 Å | ||||||||||||||||||||||||
Authors | Lu, B. / Vecchioni, S. / Ohayon, Y.P. / Seeman, N.C. / Mao, C. / Sha, R. | ||||||||||||||||||||||||
Funding support | United States, 7items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dah.cif.gz | 64.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dah.ent.gz | 41 KB | Display | PDB format |
PDBx/mmJSON format | 8dah.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dah_validation.pdf.gz | 372.5 KB | Display | wwPDB validaton report |
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Full document | 8dah_full_validation.pdf.gz | 374.1 KB | Display | |
Data in XML | 8dah_validation.xml.gz | 2.6 KB | Display | |
Data in CIF | 8dah_validation.cif.gz | 3.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/8dah ftp://data.pdbj.org/pub/pdb/validation_reports/da/8dah | 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 (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 6143.981 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 10.26 Å3/Da / Density % sol: 88.01 % |
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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: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.00743 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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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: 356.38 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 5.47→40.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 5.47→40.13 Å
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Refinement TLS params. | Method: refined / Origin x: -47.8625461798 Å / Origin y: 27.9697166215 Å / Origin z: 14.953053516 Å
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Refinement TLS group | Selection details: all |