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Yorodumi- PDB-2g92: Crystal Structure Analysis of the RNA Dodecamer CGC-(NF2)-AAUUAGC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g92 | ||||||||||||||||||
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Title | Crystal Structure Analysis of the RNA Dodecamer CGC-(NF2)-AAUUAGCG, with an Incorporated 2,4-Difluorotoluyl Residue (NF2) | ||||||||||||||||||
Components | 5'-R(*Keywords | RNA / 2 / 4-Difluorotoluyl Nucleoside / Chemical Modification / RNA Interference / Hydrogen Bonding | Function / homology | RNA / RNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | Authors | Egli, M. / Li, F. | Citation | Journal: Acs Chem.Biol. / Year: 2006 | Title: Gene silencing activity of siRNAs with a ribo-difluorotoluyl nucleotide. Authors: Xia, J. / Noronha, A. / Toudjarska, I. / Li, F. / Akinc, A. / Braich, R. / Frank-Kamenetsky, M. / Rajeev, K.G. / 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 | 2g92.cif.gz | 39.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g92.ent.gz | 29 KB | Display | PDB format |
PDBx/mmJSON format | 2g92.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/2g92 ftp://data.pdbj.org/pub/pdb/validation_reports/g9/2g92 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a duplex and corresponds to the crystallographic asymmetric unit, hence no symmetry operators are needed |
-Components
#1: RNA chain | Mass: 3828.353 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: 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: 1.95 Å3/Da / Density % sol: 36.92 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Final droplet composition: 0.5 mM oligonucleotide, 5% MPD, 20 mM sodium cacodylate, pH 5.5, 10 mM cobalt hexamine, 20 mM LiCl and 10 mM MgCl2., VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.992 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 9, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.992 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→24.8 Å / Num. all: 7538 / Num. obs: 7538 / % possible obs: 0.978 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.054 |
Reflection shell | Resolution: 1.61→1.66 Å / Rmerge(I) obs: 0.53 / % possible all: 0.969 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Model of native A-RNA Resolution: 1.61→24.78 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.698 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.11 Å2
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Refinement step | Cycle: LAST / Resolution: 1.61→24.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.61→1.648 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 4.4067 Å / Origin y: 12.3175 Å / Origin z: 14.3016 Å
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Refinement TLS group |
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