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Open data
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Basic information
Entry | Database: PDB / ID: 1ngt | ||||||||||||||||||
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Title | The Role of Minor Groove Functional Groups in DNA Hydration | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / spine of hydration / DNA conformation / modified base | Function / homology | DNA / DNA (> 10) | ![]() Method | ![]() ![]() ![]() Woods, K.K. / Lan, T. / McLaughlin, L.W. / Williams, L.D. | ![]() ![]() Title: The Role of Minor Groove Functional Groups in DNA Hydration Authors: Woods, K.K. / Lan, T. / McLaughlin, L.W. / Williams, L.D. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 24.1 KB | Display | ![]() |
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PDB format | ![]() | 15.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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: 3646.405 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-MG / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.84 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: sodium cacodylate, MPD, magnesium chloride, spermine tetrahydrochloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 22 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 163 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: CCD / Date: Jan 1, 2000 |
Radiation | Monochromator: 0.7107 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7107 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→10 Å / Num. all: 4927 / Num. obs: 4393 / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.04→2.11 Å / % possible all: 74 |
Reflection | *PLUS Lowest resolution: 10 Å / Num. measured all: 30312 / Rmerge(I) obs: 0.084 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.04→10 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection Rfree: 378 / % reflection Rfree: 22.34 % / Rfactor Rfree: 0.2815 / Rfactor Rwork: 0.2067 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.22 |