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Open data
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Basic information
Entry | Database: PDB / ID: 8tdz | |||||||||
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Title | 16mer self-complementary duplex RNA with D:U pair sequence 2 | |||||||||
![]() | RNA | |||||||||
![]() | RNA / Diaminopurine / Non-canonical base pair | |||||||||
Function / homology | COBALT HEXAMMINE(III) / RNA / RNA (> 10)![]() | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Fang, Z. / Jia, X. / Szostak, J.W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Diaminopurine in Nonenzymatic RNA Template Copying. Authors: Jia, X. / Fang, Z. / Kim, S.C. / Ding, D. / Zhou, L. / Szostak, J.W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 26.3 KB | Display | ![]() |
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PDB format | ![]() | 13.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8tdyC ![]() 8te0C ![]() 8te2C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: RNA chain | Mass: 5098.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Chemical | ChemComp-NCO / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 40 mM Lithium chloride, 20 mM Magnesium chloride hexahydrate, 40 mM Sodium cacodylate trihydrate pH 5.5, 30% v/v (+/-)-2-Methyl-2,4-pentanediol, 2 mM Hexammine cobalt(III) chloride |
-Data collection
Diffraction | Mean temperature: 99 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.64→50 Å / Num. obs: 5403 / % possible obs: 99.6 % / Redundancy: 8.7 % / Biso Wilson estimate: 7.47 Å2 / CC star: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.019 / Rrim(I) all: 0.057 / Χ2: 0.865 / Net I/σ(I): 35.5 |
Reflection shell | Resolution: 1.64→1.67 Å / Redundancy: 5 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 8.4 / Num. unique obs: 250 / CC1/2: 0.993 / CC star: 0.998 / Rpim(I) all: 0.084 / Rrim(I) all: 0.204 / Χ2: 1.059 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→41.43 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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