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Open data
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Basic information
Entry | Database: PDB / ID: 7edt | ||||||||||||||||||||||||||||
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Title | RNA duplex containing CC mispairs | ||||||||||||||||||||||||||||
![]() | RNA (5'-R(*![]() RNA / Mismatch / base pair | Function / homology | SPERMINE / RNA / RNA (> 10) | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Kondo, J. / Tada, Y. | Funding support | | ![]()
![]() ![]() Title: RNA duplex containing CC mispairs Authors: Kondo, J. / Tada, Y. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 41.5 KB | Display | ![]() |
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PDB format | ![]() | 27.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 407.5 KB | Display | ![]() |
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Full document | ![]() | 407.5 KB | Display | |
Data in XML | ![]() | 5.4 KB | Display | |
Data in CIF | ![]() | 7.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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
#1: RNA chain | Mass: 3882.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-SPM / | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: sodium cacodylate, MPD, spermine tetrahydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9204 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→19.27 Å / Num. obs: 17973 / % possible obs: 93.8 % / Redundancy: 3.85 % / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.079 / Χ2: 0.94 / Net I/σ(I): 10 / Num. measured all: 69661 / Scaling rejects: 524 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: RNA duplex constructed using Coot Resolution: 1.2→19.27 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 15.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.9 Å2 / Biso mean: 15.9171 Å2 / Biso min: 8.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.2→19.27 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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