+
Open data
-
Basic information
Entry | Database: PDB / ID: 1dc0 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF AN A/B-DNA INTERMEDIATE CATGGGCCCATG | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / A-DNA / B-DNA / INTERMEDIATE | Function / homology | DNA / DNA (> 10) | ![]() Method | ![]() ![]() ![]() Ng, H.L. / Kopka, M.L. / Dickerson, R.E. | ![]() ![]() Title: The structure of a stable intermediate in the A ;-> B DNA helix transition Authors: Ng, H.L. / Kopka, M.L. / Dickerson, R.E. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 34.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 24.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 383.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 383.1 KB | Display | |
Data in XML | ![]() | 4.1 KB | Display | |
Data in CIF | ![]() | 5.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-
Components
#1: DNA chain | Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.3 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.3MM DUPLEX DNA, 120 MM CALCIUM ACETATE, 4.8 MM SPERMINE, 60 MM SODIUM CACODYLATE BUFFER, PH 7.0, 9.5% MPD IN DROP, 25% MPD IN RESERVOIR, VAPOR DIFFUSION, SITTING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
| |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() ![]() ![]() |
Detector | Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→25 Å / Num. all: 16190 / Num. obs: 16190 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 43.6 |
Reflection shell | Resolution: 1.3→1.35 Å / Rmerge(I) obs: 0.179 / % possible all: 91.2 |
Reflection | *PLUS Num. obs: 16111 / % possible obs: 98.6 % / Num. measured all: 128129 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 90 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 7.6 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SIRAS BASED ON THE IODINATED SEQUENCE D(CAT(IODO-G)GGCCCATG) Resolution: 1.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
| |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→20 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.2 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |