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Open data
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Basic information
Entry | Database: PDB / ID: 8f2w | ||||||||||||||||||||||||||||
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Title | Structure of a B-Form Dodecamer: 5'-CGCGAATTCGCG-3 | ||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / AT sequence / Minor groove | Function / homology | DNA / DNA (> 10) | ![]() Biological species | ![]() Method | ![]() ![]() ![]() ![]() Ogbonna, E.N. / Wilson, W.D. | Funding support | | ![]()
![]() ![]() 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. #1: ![]() Title: Structure of an alternating B-DNA helix and its relationship to A-tract DNA Authors: Yoon, C. / Prive, G.G. / Goodsell, D.S. / Dickerson, R.E. / Boykin, D.W. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.5 KB | Display | ![]() |
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PDB format | ![]() | 33.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 868.3 KB | Display | ![]() |
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Full document | ![]() | 868.2 KB | Display | |
Data in XML | ![]() | 4.6 KB | Display | |
Data in CIF | ![]() | 6.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ec1C ![]() 8ed6C ![]() 8edaC ![]() 8edbC ![]() 8f1sC ![]() 8f1vC ![]() 8f20C ![]() 8f2yC ![]() 8f94C ![]() 8fb4C ![]() 8fdpC ![]() 8fdqC ![]() 8fdrC ![]() 1bnaS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (0.705840847997, -0.705948755209, -0.0585239465422), (-0.707291258126, -0.706914847883, -0.00323635923381), (-0.0390867429949, 0.0436778303264, -0.998280758935)Vector: ...NCS oper: (Code: given Matrix: (0.705840847997, -0.705948755209, -0.0585239465422), Vector: |
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Components
#1: DNA chain | Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Self-complementary native DNA dodecamer (5'-CGCGAATTCGCG-3') Source: (synth.) ![]() #2: Chemical | ChemComp-MG / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MPD, SODIUM CACODYLATE TRIHYDRATE, SPERMINE TETRACHLORIDE, SODIUM CHLORIDE, MAGNESIUM HEXAHYDRATE |
-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: Feb 2, 2021 |
Radiation | Monochromator: double crystal - LN cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→34.3 Å / Num. obs: 16736 / % possible obs: 95.2 % / Redundancy: 1.9 % / Biso Wilson estimate: 15.15 Å2 / CC1/2: 0.981 / Net I/σ(I): 16.74 |
Reflection shell | Resolution: 1.3→1.35 Å / Num. unique obs: 1649 / CC1/2: 0.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BNA Resolution: 1.3→34.29 Å / SU ML: 0.1603 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.0597 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: 20.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→34.29 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.77594464493 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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