+Open data
-Basic information
Entry | Database: PDB / ID: 3p4c | ||||||||||||||||||||
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Title | Alternatingly modified 2'Fluoro RNA octamer f/rA2U2-R32 | ||||||||||||||||||||
Components | 5'-R(*Keywords | RNA / 2'-FLUORO-RNA O2'-MODIFICATION / OCTAMER / 2'-fluoro 2'-deoxycytidine / 2'-fluoro 2'-deoxyadenosine / 2'-fluoro 2'-deoxyuridine / siRNA | Function / homology | STRONTIUM ION / RNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 Å | Authors | Pallan, P.S. / Greene, E.M. / Jicman, P.A. / Pandey, R.K. / Manoharan, M. / Rozners, E. / Egli, M. | Citation | Journal: Nucleic Acids Res. / Year: 2011 | Title: Unexpected origins of the enhanced pairing affinity of 2'-fluoro-modified RNA. Authors: Pallan, P.S. / Greene, E.M. / Jicman, P.A. / Pandey, R.K. / Manoharan, M. / Rozners, E. / Egli, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p4c.cif.gz | 30 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p4c.ent.gz | 22.1 KB | Display | PDB format |
PDBx/mmJSON format | 3p4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/3p4c ftp://data.pdbj.org/pub/pdb/validation_reports/p4/3p4c | HTTPS FTP |
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-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: 2534.525 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized modified RNA / Source: (synth.) synthetic construct (others) #2: Chemical | #3: 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: 1.83 Å3/Da / Density % sol: 32.77 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Sodium cacodylate (40 mM, pH 6.0), lithium chloride (40 mM), strontium chloride (80 mM), spermine tetrahydrochloride (12 mM), and 2-methyl-2,4-pentanediol (MPD; 10% (v/v)), equilibrated ...Details: Sodium cacodylate (40 mM, pH 6.0), lithium chloride (40 mM), strontium chloride (80 mM), spermine tetrahydrochloride (12 mM), and 2-methyl-2,4-pentanediol (MPD; 10% (v/v)), equilibrated against a reservoir of MPD (1 mL, 35%) , VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.7687 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 16, 2008 |
Radiation | Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7687 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→50 Å / Num. all: 13629 / Num. obs: 13343 / % possible obs: 97.9 % / Redundancy: 15.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 50.1 |
Reflection shell | Resolution: 1.15→1.17 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2.43 / Num. unique all: 489 / % possible all: 72.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.15→50 Å / WRfactor Rwork: 0.182 / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.15→50 Å
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Refine LS restraints |
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