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Yorodumi- PDB-4rby: First X-ray structure of RNA containing guanosine phosphorodithioate -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rby | ||||||||||||||||||||
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Title | First X-ray structure of RNA containing guanosine phosphorodithioate | ||||||||||||||||||||
Components | 5'-R(*Keywords | RNA / phosphorodithioate RNA / guanosine phosphorodithioate / phosphorothioate / guanosine analogue / hydrophobic / backbone | Function / homology | STRONTIUM ION / RNA / RNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å | Authors | Pallan, P.S. / Egli, M. | Citation | Journal: To be Published | Title: Crystal Structure, Stability and siRNA Activity of Phosphorodithioate-Modified RNAs Authors: Pallan, P.S. / Yang, X. / Sierant, M. / Abeydeera, N.D. / Hassell, T. / Martinez, C. / Janicka, M. / Nawrot, B. / Egli, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rby.cif.gz | 20.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rby.ent.gz | 11.6 KB | Display | PDB format |
PDBx/mmJSON format | 4rby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rb/4rby ftp://data.pdbj.org/pub/pdb/validation_reports/rb/4rby | HTTPS FTP |
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-Related structure data
Related structure data | 4rbzC 4rc0C 2q1rS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 3885.507 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Guanosine phosphorodithioate RNA / Source: (synth.) synthetic construct (others) | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20 mM sodium cacodylate, 40 mM sodium chloride, 10 mM barium chloride, 6 mM spermine tetrahydrochloride, 5% v/v MPD, pH 7.0, 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-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 11, 2012 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→50 Å / Num. all: 11477 / Num. obs: 11213 / % possible obs: 97.7 % / Observed criterion σ(I): 5 / Redundancy: 7 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 16.49 |
Reflection shell | Resolution: 1.19→1.23 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.037 / Mean I/σ(I) obs: 20.71 / Num. unique all: 1012 / % possible all: 88.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Q1R Resolution: 1.19→50 Å / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.19→50 Å
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Refine LS restraints |
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