+Open data
-Basic information
Entry | Database: PDB / ID: 5v1l | |||||||||||||||||||||||
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Title | Structure of S-GNA dodecamer | |||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / Glycol Nucleic Acid / GNA / RNA X-ray structure / Nuclease Stability / modified RNA | Function / homology | SPERMINE / STRONTIUM ION / RNA / RNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å | Authors | Pallan, P.S. / Egli, M. | Citation | Journal: J. Am. Chem. Soc. / Year: 2017 | Title: Chirality Dependent Potency Enhancement and Structural Impact of Glycol Nucleic Acid Modification on siRNA. Authors: Schlegel, M.K. / Foster, D.J. / Kel'in, A.V. / Zlatev, I. / Bisbe, A. / Jayaraman, M. / Lackey, J.G. / Rajeev, K.G. / Charisse, K. / Harp, J. / Pallan, P.S. / Maier, M.A. / Egli, M. / Manoharan, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5v1l.cif.gz | 84.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v1l.ent.gz | 63.4 KB | Display | PDB format |
PDBx/mmJSON format | 5v1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5v1l_validation.pdf.gz | 404.9 KB | Display | wwPDB validaton report |
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Full document | 5v1l_full_validation.pdf.gz | 413 KB | Display | |
Data in XML | 5v1l_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | 5v1l_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/5v1l ftp://data.pdbj.org/pub/pdb/validation_reports/v1/5v1l | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: RNA chain | Mass: 3807.351 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-SR / #3: Chemical | ChemComp-SPM / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Oligonucleotide (0.6 mM), sodium cacodylate (20 mM, pH 6.0), lithium chloride (20 mM), strontium chloride (40 mM), magnesium chloride (10 mM), spermine tetrahydrochloride (6 mM), and 2- ...Details: Oligonucleotide (0.6 mM), sodium cacodylate (20 mM, pH 6.0), lithium chloride (20 mM), strontium chloride (40 mM), magnesium chloride (10 mM), spermine tetrahydrochloride (6 mM), and 2-methyl-2,4-pentanediol (MPD; 5% (v/v) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→27.6 Å / Num. obs: 40705 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Net I/σ(I): 32.34 |
-Processing
Software |
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Refinement | Resolution: 1.2→27.6 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 1.2→27.6 Å
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