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Open data
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Basic information
Entry | Database: PDB / ID: 2org | ||||||
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Title | Directing Macromolecular Conformation Through Halogen Bonds | ||||||
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![]() | DNA / DNA Holliday Junction / Halogen Bond | ||||||
Function / homology | DNA![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Voth, A.R. / Hays, F.A. / Ho, P.S. | ||||||
![]() | ![]() Title: Directing macromolecular conformation through halogen bonds. Authors: Voth, A.R. / Hays, F.A. / 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 | ![]() | 22.2 KB | Display | ![]() |
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PDB format | ![]() | 13.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2orfC ![]() 2orhC ![]() 1p54S 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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Unit cell |
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Components on special symmetry positions |
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Details | The second half of the biological assembly (the Holliday junction) is generated by the two fold rotation: -x, y, -z+1 |
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Components
#1: DNA chain | Mass: 3125.874 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetically prepared decanucleotide sequences. |
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#2: DNA chain | Mass: 3029.994 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.42 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 25 mM sodium cacodylate, 20 mM calcium chloride, 1.2 mM spermine, and 0.35 mM of each DNA strand., pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 133 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 13, 2004 / Details: Osmic mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→18.2 Å / Num. all: 3852 / Num. obs: 3362 / % possible obs: 87.3 % / Redundancy: 2.4 % / Biso Wilson estimate: 5.9 Å2 / Rmerge(I) obs: 0.049 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 2.3 / Num. unique all: 382 / % possible all: 49.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1P54 Resolution: 2→18.2 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 43547.84 / Data cutoff high rms absF: 43547.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 94.7022 Å2 / ksol: 0.357361 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→18.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 6
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Xplor file |
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