+
Open data
-
Basic information
Entry | Database: PDB / ID: 8tdy | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 16mer self-complementary duplex RNA with D:U pair sequence 1 | |||||||||
![]() | RNA | |||||||||
![]() | RNA / Diaminopurine / Non-canonical base pair | |||||||||
Function / homology | RNA / RNA (> 10)![]() | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Fang, Z. / Jia, X. / Szostak, J.W. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Diaminopurine in Nonenzymatic RNA Template Copying. Authors: Jia, X. / Fang, Z. / Kim, S.C. / Ding, D. / Zhou, L. / Szostak, J.W. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 26.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 13.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 382.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 382.3 KB | Display | |
Data in XML | ![]() | 3.5 KB | Display | |
Data in CIF | ![]() | 4.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8tdzC ![]() 8te0C ![]() 8te2C C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
|
-
Components
#1: RNA chain | Mass: 5098.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.44 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 80 mM Strontium chloride hexahydrate, 20 mM Magnesium chloride hexahydrate, 40 mM Sodium cacodylate trihydrate pH 7.0, 20% v/v (+/-)-2-Methyl-2,4-pentanediol, 12 mM Spermine |
-Data collection
Diffraction | Mean temperature: 99 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.038413 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 5058 / % possible obs: 99.6 % / Redundancy: 8.5 % / Biso Wilson estimate: 10.08 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.035 / Rrim(I) all: 0.104 / Χ2: 0.951 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 483 / CC1/2: 0.902 / CC star: 0.974 / Rpim(I) all: 0.225 / Rrim(I) all: 0.569 / Χ2: 1.021 / % possible all: 99.2 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→41.68 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|