+Open data
-Basic information
Entry | Database: PDB / ID: 3s8u | ||||||
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Title | Crystal structure of a 2-azido-adenine-modified RNA | ||||||
Components | Ecoli 23 S rRNA Sarcin Ricin loop | ||||||
Keywords | RNA / hairpin RNA / RNA labelling / 2'-azido-adenine | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Ennifar, E. / Micura, R. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2012 Title: 2'-Azido RNA, a Versatile Tool for Chemical Biology: Synthesis, X-ray Structure, siRNA Applications, Click Labeling. Authors: Fauster, K. / Hartl, M. / Santner, T. / Aigner, M. / Kreutz, C. / Bister, K. / Ennifar, E. / Micura, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s8u.cif.gz | 55 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s8u.ent.gz | 41.5 KB | Display | PDB format |
PDBx/mmJSON format | 3s8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3s8u_validation.pdf.gz | 386.3 KB | Display | wwPDB validaton report |
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Full document | 3s8u_full_validation.pdf.gz | 390.9 KB | Display | |
Data in XML | 3s8u_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | 3s8u_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s8/3s8u ftp://data.pdbj.org/pub/pdb/validation_reports/s8/3s8u | HTTPS FTP |
-Related structure data
Related structure data | 3s7cC 3dvzS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: RNA chain | Mass: 8770.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
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#2: 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: 1.9 Å3/Da / Density % sol: 35.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1 volume of [3.1M (NH4)2SO4, 50mM MOPS pH7.0, 10mM MgCl2, 10mM MnCl2] + 2 volumes of [RNA in 1mM EDTA, 10mM Tris pH8.0], VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2011 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→30 Å / Num. all: 20495 / Num. obs: 19989 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.114 |
Reflection shell | Resolution: 1.2→1.23 Å / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.67 / Num. unique all: 1549 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DVZ Resolution: 1.2→27.574 Å / SU ML: 0.13 / σ(F): 2.01 / Phase error: 15.68 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.085 Å2 / ksol: 0.456 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.2→27.574 Å
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Refine LS restraints |
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LS refinement shell |
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