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- PDB-3gjj: crystal structure of a DNA duplex containing 7,8-dihydropyridol[2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gjj | ||||||||||||||||||
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Title | crystal structure of a DNA duplex containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one | ||||||||||||||||||
![]() | 5'-D(*![]() ![]() Function / homology | Chem-HT / | ![]() ![]() Method | ![]() ![]() ![]() ![]() Takenaka, A. / Juan, E.C.M. / Shimizu, S. / Haraguchi, T. / Xiao, M. / Kurose, T. / Ohkubo, A. / Sekine, M. / Shibata, T. / Millington, C.L. / Williams, D.M. | ![]() ![]() Title: Insights into the stabilizing contributions of bicyclic cytosine analogues: crystal structures of DNA duplexes containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one Authors: Takenaka, A. / Juan, E.C.M. / Shimizu, S. / Haraguchi, T. / Xiao, M. / Kurose, T. / Ohkubo, A. / Sekine, M. / Shibata, T. / Millington, M. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 25.5 KB | Display | ![]() |
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PDB format | ![]() | 16.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3gjhC ![]() 3gjkC ![]() 3gjlC ![]() 1dnhS 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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Unit cell |
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Components
#1: DNA chain | Mass: 3686.429 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-HT / | ![]() #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: 46.12 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.60mM ssDNA, 20mM Sodium cacodylate (pH6.0), 6mM Spermine tetrahydrochloride, 40mM Potassium chloride, 6mM Sodium chloride, 0.2% CHAPS, 0.30mM Hoechst33258, 5% MPD , VAPOR DIFFUSION, ...Details: 0.60mM ssDNA, 20mM Sodium cacodylate (pH6.0), 6mM Spermine tetrahydrochloride, 40mM Potassium chloride, 6mM Sodium chloride, 0.2% CHAPS, 0.30mM Hoechst33258, 5% MPD , VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 26, 2008 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.9→50 Å / Num. all: 1714 / Num. obs: 1714 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 69.6 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 10.8 / Num. unique all: 169 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1DNH Resolution: 2.9→9.9 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
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Displacement parameters | Biso mean: 43.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→9.9 Å
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LS refinement shell | Resolution: 2.9→3.08 Å
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