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Open data
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Basic information
Entry | Database: PDB / ID: 8f94 | ||||||
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Title | Structure of an alternating AT 16-mer: 5'-GCTGGATATATCCAGC-3 | ||||||
![]() | DNA 16-mer | ||||||
![]() | DNA / AT sequence / Minor groove | ||||||
Function / homology | DNA / DNA (> 10)![]() | ||||||
Biological species | DNA molecule (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Terrell, J.R. / Ogbonna, E.N. / Wilson, W.D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: X-ray Structure Characterization of the Selective Recognition of AT Base Pair Sequences. Authors: Ogbonna, E.N. / Paul, A. / Farahat, A.A. / Terrell, J.R. / Mineva, E. / Ogbonna, V. / Boykin, D.W. / Wilson, W.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44.3 KB | Display | ![]() |
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PDB format | ![]() | 25.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.3 MB | Display | ![]() |
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Full document | ![]() | 5.3 MB | Display | |
Data in XML | ![]() | 4 KB | Display | |
Data in CIF | ![]() | 5.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ec1C ![]() 8ed6C ![]() 8edaC ![]() 8edbC ![]() 8f1sC ![]() 8f1vC ![]() 8f20C ![]() 8f2wC ![]() 8f2yC ![]() 8fb4C ![]() 8fdpC ![]() 8fdqC ![]() 8fdrC 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 on special symmetry positions |
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Components
#1: DNA chain | Mass: 4898.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others) | ||||
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#2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.85 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 1 mM DNA duplex annealed in 7.5 mM HEPES, pH=6.6 mixed at a 1:1 ratio with well solution containing 10 mM HEPES, pH=8.6, 600 mM CaCl2, 38% PEG200 |
-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: Sep 28, 2022 |
Radiation | Monochromator: Horizontal double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→26.63 Å / Num. obs: 20060 / % possible obs: 98.5 % / Redundancy: 2 % / Biso Wilson estimate: 15.5 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.01722 / Rpim(I) all: 0.01722 / Rrim(I) all: 0.02436 / Net I/σ(I): 22.55 |
Reflection shell | Resolution: 1.08→1.119 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1479 / Mean I/σ(I) obs: 6.48 / Num. unique obs: 1882 / CC1/2: 0.939 / CC star: 0.984 / Rpim(I) all: 0.1479 / Rrim(I) all: 0.2092 / % possible all: 92.88 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 21.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.08→26.63 Å
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Refine LS restraints |
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LS refinement shell |
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