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Open data
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Basic information
Entry | Database: PDB / ID: 7sb8 | ||||||
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Title | d(GA(CGA)5) parallel-stranded homo-duplex | ||||||
![]() | GA(CGA)5 | ||||||
![]() | DNA / triplet repeat DNA / parallel-stranded duplex / non-canonical DNA / d(CGA) | ||||||
Function / homology | COBALT HEXAMMINE(III) / STRONTIUM ION / DNA / DNA (> 10)![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Luteran, E.M. / Paukstelis, P.J. | ||||||
Funding support | 1items
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![]() | ![]() 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 | ![]() | 127.8 KB | Display | ![]() |
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PDB format | ![]() | 98.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 405.2 KB | Display | ![]() |
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Full document | ![]() | 405.2 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7t6yC ![]() 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 5255.427 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-SR / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-NCO / #5: 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: 1.72 Å3/Da / Density % sol: 28.33 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 8% PEG400, 96 mM strontium chloride, 32 mM lithium chloride, 8 mM hexamminecobalt(III) chloride, 24 mM sodium cacodylate, equilibrated against 30% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.317→90.41 Å / Num. obs: 48232 / % possible obs: 94.7 % / Redundancy: 4.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.049 / Rrim(I) all: 0.106 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.317→1.34 Å / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 2 / Num. unique obs: 2175 / CC1/2: 0.82 / Rpim(I) all: 0.35 / Rrim(I) all: 0.757 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1IXJ Resolution: 1.317→90.409 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.35 / 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: 233.18 Å2 / Biso mean: 19.4304 Å2 / Biso min: 3.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.317→90.409 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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