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- PDB-1d8g: ULTRAHIGH RESOLUTION CRYSTAL STRUCTURE OF B-DNA DECAMER D(CCAGTACTGG) -
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Open data
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Basic information
Entry | Database: PDB / ID: 1d8g | ||||||||||||||||||
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Title | ULTRAHIGH RESOLUTION CRYSTAL STRUCTURE OF B-DNA DECAMER D(CCAGTACTGG) | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / B-DNA / ALTERNATE CONFORMATION / ULTRAHIGH RESOLUTION / TRP REPRESSOR / POLYAMIDE | Function / homology | DNA | ![]() Method | ![]() ![]() ![]() Kielkopf, C.L. / Ding, S. / Kuhn, P. / Rees, D.C. | ![]() ![]() Title: Conformational flexibility of B-DNA at 0.74 A resolution: d(CCAGTACTGG)(2). Authors: Kielkopf, C.L. / Ding, S. / Kuhn, P. / Rees, D.C. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 29.3 KB | Display | ![]() |
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PDB format | ![]() | 19.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 378.9 KB | Display | ![]() |
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Full document | ![]() | 382.8 KB | Display | |
Data in XML | ![]() | 5.2 KB | Display | |
Data in CIF | ![]() | 6.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 3045.004 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.81 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: MPD, CALCIUM ACETATE, TRIS(HYDROXYAMINOMETHANE) BUFFER, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 0.74→16 Å / Num. all: 29991 / Num. obs: 29991 / % possible obs: 90 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 26.7 | ||||||||||||||||||||||||
Reflection shell | Resolution: 0.74→0.75 Å / Rmerge(I) obs: 0.239 / % possible all: 71.1 | ||||||||||||||||||||||||
Reflection | *PLUS Num. measured all: 130259 | ||||||||||||||||||||||||
Reflection shell | *PLUS % possible obs: 71.1 % / Mean I/σ(I) obs: 6.9 |
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Processing
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Refinement | Resolution: 0.74→16 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: SADI RESTRAINTS ON BACKBONE
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Refinement step | Cycle: LAST / Resolution: 0.74→16 Å
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 28208 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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