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Open data
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Basic information
Entry | Database: PDB / ID: 7t6y | |||||||||||||||||||||||||||||||
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Title | d((CGA)5TGA) parallel-stranded homo-duplex | |||||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / triplet repeat DNA / parallel-stranded duplex / non-canonical DNA / d(CGA) | Function / homology | : / DNA / DNA (> 10) | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Luteran, E.M. / Paukstelis, P.J. | Funding support | 1items |
![]() ![]() Title: The parallel-stranded d(CGA) duplex is a highly predictable structural motif with two conformationally distinct strands. Authors: Luteran, E.M. / Paukstelis, P.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 | ![]() | 37.1 KB | Display | ![]() |
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PDB format | ![]() | 22.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 377.2 KB | Display | ![]() |
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Full document | ![]() | 377.3 KB | Display | |
Data in XML | ![]() | 5.2 KB | Display | |
Data in CIF | ![]() | 6.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7sb8C ![]() 1ixjS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: DNA chain | Mass: 5559.620 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) #2: Chemical | ChemComp-BA / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.95 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20% MPD, 120 mM barium chloride, 30 mM sodium cacodylate, equilibrated against 30% MPD |
-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: Nov 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→32.255 Å / Num. obs: 3487 / % possible obs: 87.2 % / Redundancy: 1.8 % / CC1/2: 0.94 / Rpim(I) all: 0.109 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Mean I/σ(I) obs: 5 / Num. unique obs: 350 / CC1/2: 0.395 / Rpim(I) all: 0.288 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1IXJ Resolution: 2.3→32.255 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 19.5 / Stereochemistry target values: ML
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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: 41.02 Å2 / Biso mean: 13.2239 Å2 / Biso min: 1.79 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→32.255 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 87 %
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