+
Open data
-
Basic information
Entry | Database: PDB / ID: 3p4b | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Alternatingly modified 2'Fluoro RNA octamer f/rA2U2-P3 | ||||||||||||||||||
![]() | 5'-R(*![]() RNA / 2'-FLUORO-RNA / O2'-MODIFICATION / OCTAMER / 2'-fluoro 2'-deoxycytidine / 2'-fluoro 2'-deoxyadenosine / 2'-fluoro 2'-deoxyuridine / siRNA | Function / homology | : / RNA | ![]() Method | ![]() ![]() ![]() ![]() Pallan, P.S. / Greene, E.M. / Jicman, P.A. / Pandey, R.K. / Manoharan, M. / Rozners, E. / Egli, M. | ![]() ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 68.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 55.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 436.2 KB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 10.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3p4aSC ![]() 3p4cC ![]() 3p4dC C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||||||||||||||
2 | ![]()
| |||||||||||||||||||||
3 | ![]()
| |||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||
Components on special symmetry positions |
|
-
Components
#1: RNA chain | Mass: 2534.525 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: Chemically synthesized modified RNA octamer #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.55 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Sodium cacodylate (40 mM, pH 6.0), sodium chloride (80 mM), barium chloride (20 mM), spermine tetrahydrochloride (12 mM), and 2-methyl-2,4-pentanediol (MPD; 10% (v/v)), equilibrated against ...Details: Sodium cacodylate (40 mM, pH 6.0), sodium chloride (80 mM), barium chloride (20 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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 17, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. all: 22793 / Num. obs: 21294 / % possible obs: 98.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 39 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.34 / Num. unique all: 1005 / % possible all: 81.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3P4A Resolution: 1.45→21.69 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.288 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.807 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→21.69 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|