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Open data
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Basic information
Entry | Database: PDB / ID: 1zf9 | ||||||||||||||||||
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Title | GGG Duplex A-DNA | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / Crystallographic Screen / DNA Structure / Holliday Junction / Molecular Structure | Function / homology | DNA | ![]() Method | ![]() ![]() ![]() ![]() Hays, F.A. / Teegarden, A.T. / Jones, Z.J.R. / Harms, M. / Raup, D. / Watson, J. / Cavaliere, E. / Ho, P.S. | ![]() ![]() Title: How sequence defines structure: a crystallographic map of DNA structure and conformation. Authors: Hays, F.A. / Teegarden, A. / Jones, Z.J. / Harms, M. / Raup, D. / Watson, J. / Cavaliere, E. / Ho, P.S. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 23.7 KB | Display | ![]() |
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PDB format | ![]() | 15.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 389.3 KB | Display | ![]() |
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Full document | ![]() | 396.1 KB | Display | |
Data in XML | ![]() | 5.6 KB | Display | |
Data in CIF | ![]() | 7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zewC ![]() 1zexC ![]() 1zeyC ![]() 1zezC ![]() 1zf0C ![]() 1zf1C ![]() 1zf2C ![]() 1zf3C ![]() 1zf4C ![]() 1zf5C ![]() 1zf6C ![]() 1zf7C ![]() 1zf8C ![]() 1zfaC ![]() 1zfbC ![]() 1zfcC ![]() 1zfeC ![]() 1zffC ![]() 1zfgC ![]() 1zfhC ![]() 1zfmC C: citing same article ( |
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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
#1: DNA chain | Mass: 3046.980 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: DNA WAS SYNTHESIZED ON AN APPLIED BIOSYSTEMS DNA SYNTHESIZER USING PHOSPHORAMIDITE CHEMISTRY, WITH THE TRITYL-PROTECTING GROUP LEFT INTACT AT THE 5'-TERMINAL NUCLEOTIDE THEN DEPROTECTED BY ...Details: DNA WAS SYNTHESIZED ON AN APPLIED BIOSYSTEMS DNA SYNTHESIZER USING PHOSPHORAMIDITE CHEMISTRY, WITH THE TRITYL-PROTECTING GROUP LEFT INTACT AT THE 5'-TERMINAL NUCLEOTIDE THEN DEPROTECTED BY TREATMENT WITH 3% ACETIC ACID FOR FIFTEEN MINUTES, NEUTRALIZED WITH AMMONIUM HYDROXIDE, AND DESALTED ON A SIGMA G-25 SEPHADEX COLUMN. #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.22 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / pH: 7 Details: Na Cacodylate, CaCl2, Spermine, MPD in resevoir, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.00 | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.35→99 Å / Num. obs: 10745 / % possible obs: 92.2 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 5 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 29.4 | ||||||||||||||||||
Reflection shell | Resolution: 1.35→1.4 Å / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2 / % possible all: 48.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: ndb entry ADJ049 Resolution: 1.38→18.99 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 53828.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: STRUCTURE NOT REFINED TO ITS LOWEST R AND RFREE VALUES. PLEASE REFER TO CITATION ABOVE FOR MORE DETAILS.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 80.17 Å2 / ksol: 0.7443 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 6.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.38→18.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.38→1.47 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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