+
Open data
-
Basic information
Entry | Database: PDB / ID: 1d30 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | THE STRUCTURE OF DAPI BOUND TO DNA | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | 6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE / DNA / DNA (> 10) | ![]() Method | ![]() ![]() Larsen, T. / Goodsell, D.S. / Cascio, D. / Grzeskowiak, K. / Dickerson, R.E. | ![]() ![]() Title: The structure of DAPI bound to DNA. Authors: Larsen, T.A. / Goodsell, D.S. / Cascio, D. / Grzeskowiak, K. / Dickerson, R.E. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 26.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 14.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
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: Chemical | ChemComp-DAP / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.5 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, temperature 277.00K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
| |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Ambient temp details: ROOM TEMPERATURE |
---|---|
Detector | Type: SDMS / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.4 Å / Num. all: 9292 / Num. obs: 2541 |
Reflection | *PLUS Rmerge(I) obs: 0.116 |
-
Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.4→10 Å / σ(F): 2 /
| ||||||||||||
Refine Biso |
| ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
| ||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 10 Å / Num. reflection all: 2541 / Num. reflection obs: 2428 / σ(F): 2 / Rfactor obs: 0.222 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |