+Open data
-Basic information
Entry | Database: PDB / ID: 7sg8 | |||||||||||||||||||||
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Title | [T-T] DNA mismatch in a self-assembling rhombohedral lattice | |||||||||||||||||||||
Components |
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Keywords | DNA / Tensegrity triangle / self-assembling crystal / metal-mediated mismatch | |||||||||||||||||||||
Function / homology | DNA / DNA (> 10) Function and homology information | |||||||||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.71 Å | |||||||||||||||||||||
Authors | Vecchioni, S. / Lu, B. / Bernfeld, W. / Seeman, N.C. / Sha, R. / Ohayon, Y.P. | |||||||||||||||||||||
Funding support | United States, 6items
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Citation | Journal: Adv Mater / Year: 2023 Title: Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction. Authors: Vecchioni, S. / Lu, B. / Livernois, W. / Ohayon, Y.P. / Yoder, J.B. / Yang, C.F. / Woloszyn, K. / Bernfeld, W. / Anantram, M.P. / Canary, J.W. / Hendrickson, W.A. / Rothschild, L.J. / Mao, C. ...Authors: Vecchioni, S. / Lu, B. / Livernois, W. / Ohayon, Y.P. / Yoder, J.B. / Yang, C.F. / Woloszyn, K. / Bernfeld, W. / Anantram, M.P. / Canary, J.W. / Hendrickson, W.A. / Rothschild, L.J. / Mao, C. / Wind, S.J. / Seeman, N.C. / Sha, R. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sg8.cif.gz | 68.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sg8.ent.gz | 43.1 KB | Display | PDB format |
PDBx/mmJSON format | 7sg8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sg/7sg8 ftp://data.pdbj.org/pub/pdb/validation_reports/sg/7sg8 | HTTPS FTP |
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-Related structure data
Related structure data | 7sd6C 7sd7C 7sd8C 7sdfC 7sdgC 7sdhC 7sdiC 7sdjC 7sdkC 7sdlC 7sdmC 7sdnC 7sdoC 7sdqC 7sdsC 7sdtC 7sduC 7sdvC 7sdwC 7sdxC 7sdyC 7sdzC 7se0C 7se1C 7se2C 7se3C 7se4C 7se5C 7sg9C 7sgaC 7sgbC 5w6wS C: citing same article (ref.) S: Starting model for refinement |
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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: 6463.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 2066.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 2129.409 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: 8.41 Å3/Da / Description: Rhombohedral |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: MOPS, Magnesium sulfate / 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: Oct 24, 2020 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1.00743 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 3.71→66.16 Å / Num. obs: 3226 / % possible obs: 89.4 % / Redundancy: 11.4 % / Biso Wilson estimate: 227.38 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.6 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5W6W Resolution: 3.71→33.08 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.9876 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: 234.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.71→33.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.71→33.08 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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