[English] 日本語
![](img/lk-miru.gif)
- PDB-115d: ORDERED WATER STRUCTURE IN AN A-DNA OCTAMER AT 1.7 ANGSTROMS RESO... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 115d | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | ORDERED WATER STRUCTURE IN AN A-DNA OCTAMER AT 1.7 ANGSTROMS RESOLUTION | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / A-DNA / DOUBLE HELIX / MODIFIED | Function / homology | DNA | ![]() Method | ![]() ![]() ![]() Kennard, O. / Cruse, W.B.T. / Nachman, J. / Prange, T. / Shakked, Z. / Rabinovich, D. | ![]() ![]() Title: Ordered water structure in an A-DNA octamer at 1.7 A resolution. Authors: Kennard, O. / Cruse, W.B. / Nachman, J. / Prange, T. / Shakked, Z. / Rabinovich, D. #1: ![]() Title: Coexistence of A-and B-Form DNA in a Single Crystal Lattice Authors: Doucet, J. / Benoit, J.-P. / Cruse, W.B.T. / Prange, T. / Kennard, O. #2: ![]() Title: Sequence-Dependent Conformation of an A-DNA Double Helix. The Crystal Structure of the Octamer d(G-G-T-A-T-A-C-C) Authors: Shakked, Z. / Rabinovich, D. / Kennard, O. / Cruse, W.B.T. / Salisbury, S.A. / Viswamitra, M.A. #3: ![]() Title: Crystalline A-DNA. The X-Ray Analysis of the Fragment d(G-G-T-A-T-A-C-C) Authors: Shakked, Z. / Rabinovich, D. / Cruse, W.B.T. / Egert, E. / Kennard, O. / Sala, G. / Salisbury, S.A. / Viswamitra, M.A. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 18.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 12.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 329.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 332.8 KB | Display | |
Data in XML | ![]() | 2.4 KB | Display | |
Data in CIF | ![]() | 3.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: DNA chain | Mass: 2556.357 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.62 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION | |||||||||||||||||||||||||||||||||||
Components of the solutions |
| |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||
Detector |
| ||||||||||||
Radiation |
| ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Highest resolution: 1.7 Å / Num. obs: 4669 / Observed criterion σ(F): 2 | ||||||||||||
Reflection | *PLUS Highest resolution: 1.7 Å / Num. all: 5833 / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.097 |
-
Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.7→10 Å / σ(F): 2 /
| ||||||||||||
Refine Biso |
| ||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
| ||||||||||||
Software | *PLUS Name: NUCLSQ / Classification: refinement | ||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.14 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
|