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Open data
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Basic information
Entry | Database: PDB / ID: 6zrl | |||||||||
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Title | Racemic compound of RNA duplexes. | |||||||||
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![]() | RNA / racemic compound | |||||||||
Function / homology | RNA![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rypniewski, W. | |||||||||
![]() | ![]() Title: Broken symmetry between RNA enantiomers in a crystal lattice. Authors: Kiliszek, A. / Blaszczyk, L. / Bejger, M. / Rypniewski, 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 | ![]() | 37.6 KB | Display | ![]() |
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PDB format | ![]() | 25.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419.3 KB | Display | ![]() |
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Full document | ![]() | 420.5 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 8.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zpfC ![]() 6zq9SC ![]() 6zr1C ![]() 6zrsC ![]() 6zw3C ![]() 6zwuC ![]() 6zx5C ![]() 6zx8C ![]() 7a9lC ![]() 7a9nC ![]() 7a9oC ![]() 7a9pC ![]() 7a9qC ![]() 7a9rC ![]() 7a9sC ![]() 7a9tC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-RNA chain , 4 types, 4 molecules KLMN
#1: RNA chain | Mass: 2597.601 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chain K is L-enantiomer. It pairs with chain L. / Source: (synth.) ![]() ![]() |
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#2: RNA chain | Mass: 2517.553 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chain L is L-enantiomer. It pairs with chain K. / Source: (synth.) ![]() ![]() |
#3: RNA chain | Mass: 2597.601 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chain M is D-enantiomer. It pairs with chain N. / Source: (synth.) ![]() ![]() |
#4: RNA chain | Mass: 2517.553 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chain N is D-enantiomer. It pairs with chain M. / Source: (synth.) ![]() ![]() |
-Non-polymers , 2 types, 191 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-ZN / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.76 % / Description: needle |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M zinc acetate, 0.1 M cacodylate buffer, 18% w/v polyehylene glycol 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.283 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→37 Å / Num. obs: 10704 / % possible obs: 88.9 % / Redundancy: 5.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.118 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 1.53→1.62 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.731 / Num. unique obs: 1474 / CC1/2: 0.862 / Rrim(I) all: 0.81 / % possible all: 75.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ZQ9 Resolution: 1.53→36.966 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.461 / SU ML: 0.087 / Cross valid method: FREE R-VALUE / ESU R: 0.125 / ESU R Free: 0.13 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.568 Å2
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Refinement step | Cycle: LAST / Resolution: 1.53→36.966 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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