+Open data
-Basic information
Entry | Database: PDB / ID: 8te2 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 16mer self-complementary duplex RNA with D:C pair sequence 2 | |||||||||
Components | RNA | |||||||||
Keywords | RNA / Diaminopurine / Non-canonical base pair | |||||||||
Function / homology | RNA / RNA (> 10) Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | |||||||||
Authors | Fang, Z. / Jia, X. / Szostak, J.W. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2024 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8te2.cif.gz | 26.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8te2.ent.gz | 13.2 KB | Display | PDB format |
PDBx/mmJSON format | 8te2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8te2_validation.pdf.gz | 395.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8te2_full_validation.pdf.gz | 397.7 KB | Display | |
Data in XML | 8te2_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | 8te2_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/8te2 ftp://data.pdbj.org/pub/pdb/validation_reports/te/8te2 | HTTPS FTP |
-Related structure data
Related structure data | 8tdyC 8tdzC 8te0C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: RNA chain | Mass: 5097.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.84 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 400 mM Sodium chloride, 120 mM Calcium chloride, 27% v/v (+/-)-2-Methyl-2,4-pentanediol, 20 mM MES pH 5.8 |
-Data collection
Diffraction | Mean temperature: 99 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 2.0.1 / Wavelength: 1.038413 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 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: 1.63→41.79 Å / Num. obs: 5477 / % possible obs: 99.7 % / Redundancy: 8.3 % / Biso Wilson estimate: 18.44 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.048 / Rrim(I) all: 0.105 / Χ2: 0.85 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.63→1.66 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 285 / CC1/2: 0.982 / Rpim(I) all: 0.216 / Rrim(I) all: 0.424 / Χ2: 0.26 / % possible all: 97.1 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→31.22 Å / SU ML: 0.1552 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.9209 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: 22.94 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→31.22 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell |
|