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- PDB-1ih1: Crystal Structure of the B-DNA Hexamer GGCGCC with Cobalt Hexamin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ih1 | ||||||||||||||||||
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Title | Crystal Structure of the B-DNA Hexamer GGCGCC with Cobalt Hexamine Resolved to 2.0 Angstroms | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / B to A DNA transition / DNA transition / structural transition | Function / homology | COBALT HEXAMMINE(III) / DNA | ![]() Method | ![]() ![]() ![]() Vargason, J.M. / Henderson, K. / Ho, P.S. | ![]() ![]() Title: A crystallographic map of the transition from B-DNA to A-DNA. Authors: Vargason, J.M. / Henderson, K. / 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 | ![]() | 15.5 KB | Display | ![]() |
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PDB format | ![]() | 9.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 347.4 KB | Display | ![]() |
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Full document | ![]() | 347.3 KB | Display | |
Data in XML | ![]() | 2.6 KB | Display | |
Data in CIF | ![]() | 3.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-MG / | #3: Chemical | ChemComp-NCO / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.78 Å3/Da / Density % sol: 67.44 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: magnesium chloride, sodium cacodylate, spermine tetrahydrochloride, cobalt hexamine, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 6 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 26, 2000 / Details: mirrors |
Radiation | Monochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→99 Å / Num. all: 4225 / Num. obs: 4225 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 52.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.426 / % possible all: 95 |
Reflection | *PLUS Num. measured all: 18846 |
Reflection shell | *PLUS % possible obs: 95 % |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: G.Parkinson, J.Vojtechovsky, L.Clowney, A.T.Brunger, H.M.Berman
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.228 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |