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- PDB-8eg4: [iU:Ag+:iU] Metal-mediated DNA base pair in a self-assembling rho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8eg4 | |||||||||||||||||||||
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Title | [iU:Ag+:iU] Metal-mediated DNA base pair in a self-assembling rhombohedral lattice | |||||||||||||||||||||
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![]() | DNA / Tensegrity triangle / self-assembling crystal / metal-mediated mismatch | |||||||||||||||||||||
Function / homology | SILVER ION / DNA / DNA (> 10)![]() | |||||||||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Vecchioni, S. / Lu, B. / Seeman, N.C. / Sha, R. / Ohayon, Y.P. | |||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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. #1: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.1 KB | Display | ![]() |
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PDB format | ![]() | 43.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 593.7 KB | Display | ![]() |
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Full document | ![]() | 598.4 KB | Display | |
Data in XML | ![]() | 3.3 KB | Display | |
Data in CIF | ![]() | 4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ul8C ![]() 8e4dC ![]() 8e4eC ![]() 3gbiS 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: 6575.054 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 2507.477 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) |
#5: Chemical | ChemComp-AG / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 7.33 Å3/Da / Density % sol: 83.22 % / Description: Rhombohedral |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM MOPS, 1.25 M magnesium sulfate, 720 uM silver nitrate Temp details: 338-293K 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: Jul 18, 2021 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.0073 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 4.18→64.307 Å / Num. obs: 3757 / % possible obs: 86.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 274.65 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.4 | |||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3GBI Resolution: 4.18→40.98 Å / SU ML: 0.8741 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 54.9711 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: 311.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.18→40.98 Å
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Refine LS restraints |
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LS refinement shell |
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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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