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Open data
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Basic information
Entry | Database: PDB / ID: 5tdj | ||||||||||||||||||||
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Title | RNA decamer duplex with four 2'-5'-linkages | ||||||||||||||||||||
![]() | RNA (5'-R(*![]() RNA / 2'-5'-LINKAGE / PLANT PROTEIN | Function / homology | STRONTIUM ION / RNA | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Luo, Z. / Sheng, J. | ![]() ![]() Title: Structural insights into RNA duplexes with multiple 2 -5 -linkages. Authors: Shen, F. / Luo, Z. / Liu, H. / Wang, R. / Zhang, S. / Gan, J. / Sheng, J. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 36.8 KB | Display | ![]() |
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PDB format | ![]() | 25 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5tdkC ![]() 4ms9S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 3206.980 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: CHEMICALLY SYNTHESIZED BY SOLID PHASE SYNTHESIS AND PURIFIED BY HPLC Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-SR / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% MPD (2-methyl-2,4-pentanediol), 40 mM sodium cacodylate pH 7.0, 12 mM spermine tetrahydrochloride, 40mM LiCl, 20 mM MgCl2 and 80 mM SrCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 7870 / % possible obs: 96.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.649 / % possible all: 88.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4MS9 Resolution: 1.5→19.9 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.98 / SU B: 3.67 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.069 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.663 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→19.9 Å
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Refine LS restraints |
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