[English] 日本語
![](img/lk-miru.gif)
- PDB-3ot0: Crystal structure of a DNA containing the rigid nitroxide spin-la... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3ot0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a DNA containing the rigid nitroxide spin-labeled nucleotide C-spin | ||||||
![]() | Spin-labeled DNA | ||||||
![]() | DNA / nitroxide / spin-label / EPR spectroscopy / fluorescence spectroscopy / modified nucleic acid / C-spin / deoxycytosine analog / phenoxazine / spectroscopic probe / PELDOR / 2'-O-methyl U | ||||||
Function / homology | DNA/RNA hybrid![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Edwards, T.E. | ||||||
![]() | ![]() Title: Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe C. Authors: Edwards, T.E. / Cekan, P. / Reginsson, G.W. / Shelke, S.A. / Ferre-D'Amare, A.R. / Schiemann, O. / Sigurdsson, S.T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 24.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 15.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 380.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 383.6 KB | Display | |
Data in XML | ![]() | 4.3 KB | Display | |
Data in CIF | ![]() | 5.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kgkS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: DNA/RNA hybrid | Mass: 3263.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical synthesis #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.51 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 1.2 mM DNA in 10% 2-methane-2,4-pentanediol (MPD), 40 mM sodium cacodylate pH 6.0, 12 mM spermine-HCl, 80 mM NaCl, 12 mM KCl, 12 mM MgCl2 against a reserviore of 35% MPD, VAPOR DIFFUSION, ...Details: 1.2 mM DNA in 10% 2-methane-2,4-pentanediol (MPD), 40 mM sodium cacodylate pH 6.0, 12 mM spermine-HCl, 80 mM NaCl, 12 mM KCl, 12 mM MgCl2 against a reserviore of 35% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 17, 2010 / Details: VariMax | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→50 Å / Num. all: 5955 / Num. obs: 5613 / % possible obs: 94.3 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.022 / Net I/σ(I): 53.95 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KGK Resolution: 1.7004→16.824 Å / SU ML: 0.17 / σ(F): 1.37 / Phase error: 19.5 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.023 Å2 / ksol: 0.406 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7004→16.824 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell |
|