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Open data
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Basic information
Entry | Database: PDB / ID: 7yvx | ||||||||||||||||||||||||||||
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Title | Left-handed DNA duplex containing consecutive G-G base pairs | ||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / Z-form / DNA nanotechnology | Function / homology | : / DNA | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Kondo, J. | Funding support | | ![]()
![]() ![]() Title: Left-handed DNA duplex containing consecutive G-G base pairs Authors: Kondo, J. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 16.2 KB | Display | ![]() |
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PDB format | ![]() | 8.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 380.2 KB | Display | ![]() |
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Full document | ![]() | 380.5 KB | Display | |
Data in XML | ![]() | 2.5 KB | Display | |
Data in CIF | ![]() | 2.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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 on special symmetry positions |
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Components
#1: DNA chain | Mass: 3165.900 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
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#2: Chemical | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: MPD, sodium chloride, hexammine cobalt chloride, sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 21, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.605 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.99→37.56 Å / Num. obs: 1553 / % possible obs: 99.7 % / Redundancy: 10.003 % / Biso Wilson estimate: 54.539 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.106 / Χ2: 1.163 / Net I/σ(I): 18.64 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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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 max: 120.24 Å2 / Biso mean: 50.3472 Å2 / Biso min: 28.95 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.99→37.56 Å
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LS refinement shell | Resolution: 2.99→3.16 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
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