+Open data
-Basic information
Entry | Database: PDB / ID: 5v2h | |||||||||||||||||||||||
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Title | RNA octamer containing glycol nucleic acid, SgnT | |||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / glycol nucleic acid | Function / homology | COBALT HEXAMMINE(III) / RNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.08001306231 Å | Authors | Harp, J.M. / 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 | 5v2h.cif.gz | 72.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v2h.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 5v2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5v2h_validation.pdf.gz | 425.9 KB | Display | wwPDB validaton report |
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Full document | 5v2h_full_validation.pdf.gz | 427.8 KB | Display | |
Data in XML | 5v2h_validation.xml.gz | 7 KB | Display | |
Data in CIF | 5v2h_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/5v2h ftp://data.pdbj.org/pub/pdb/validation_reports/v2/5v2h | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: RNA chain | Mass: 2561.448 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-NCO / | #3: Chemical | ChemComp-MG / | #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: 2.08 Å3/Da / Density % sol: 40.81 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.5 mM oligonucleotide, 40 mM sodium chloride, 10 mM magnesium chloride, 10 mM cobalt(III) hexamine chloride, 20 mM sodium cacodylate, 5% 2-methyl-2,4-pentanediol equilibrated against 40% 2- ...Details: 0.5 mM oligonucleotide, 40 mM sodium chloride, 10 mM magnesium chloride, 10 mM cobalt(III) hexamine chloride, 20 mM sodium cacodylate, 5% 2-methyl-2,4-pentanediol equilibrated against 40% 2-methyl-2-4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.91836 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91836 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→33.781 Å / Num. obs: 35479 / % possible obs: 97.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 5.18 Å2 / CC1/2: 0.969 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.069 / Net I/σ(I): 10.74 |
Reflection shell | Resolution: 1.08→1.119 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2652 / Mean I/σ(I) obs: 2.44 / Num. unique obs: 3532 / CC1/2: 0.822 / Rpim(I) all: 0.2652 / % possible all: 97.14 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.08001306231→33.7809065231 Å / SU ML: 0.0713631076248 / Cross valid method: FREE R-VALUE / σ(F): 1.42213021666 / Phase error: 15.8804008545
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.8546699308 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.08001306231→33.7809065231 Å
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Refine LS restraints |
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LS refinement shell |
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