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Open data
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Basic information
Entry | Database: PDB / ID: 1zf3 | ||||||||||||||||||
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Title | ATC Four-stranded DNA Holliday Junction | ||||||||||||||||||
![]() | 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 | ![]() | 24.8 KB | Display | ![]() |
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PDB format | ![]() | 16.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 385.1 KB | Display | ![]() |
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Full document | ![]() | 387 KB | Display | |
Data in XML | ![]() | 5.3 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 ![]() 1zf4C ![]() 1zf5C ![]() 1zf6C ![]() 1zf7C ![]() 1zf8C ![]() 1zf9C ![]() 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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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: 3045.005 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 | ChemComp-CA / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.02 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Na Cacodylate, CaCl2, Spermine, MPD in resevoir, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 26, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→99 Å / Num. obs: 4856 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Χ2: 1.034 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.84→1.92 Å / % possible obs: 96.9 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 1.07 / Num. measured obs: 465 / Rsym value: 0.626 / Χ2: 1.024 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: ndb entry UD0058 Resolution: 1.84→30.08 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.851 / SU B: 6.34 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.615 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→30.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.888 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Label seq-ID: 1 - 10
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