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- PDB-4rkv: Structural variations and solvent structure of UGGGGU quadruplexe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rkv | ||||||||||||||||||||
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Title | Structural variations and solvent structure of UGGGGU quadruplexes stabilized by Sr2+ ions | ||||||||||||||||||||
![]() | RNA (5'-R(*![]() RNA / RNA quadruplexes / parallel-stranded | Function / homology | STRONTIUM ION / RNA | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Fyfe, A.C. / Dunten, P.W. / Scott, W.G. | ![]() ![]() Title: Structural Variations and Solvent Structure of r(UGGGGU) Quadruplexes Stabilized by Sr(2+) Ions. Authors: Fyfe, A.C. / Dunten, P.W. / Martick, M.M. / Scott, W.G. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 29 KB | Display | ![]() |
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PDB format | ![]() | 21.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 400.9 KB | Display | ![]() |
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Full document | ![]() | 401.1 KB | Display | |
Data in XML | ![]() | 3.5 KB | Display | |
Data in CIF | ![]() | 4.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: RNA chain | Mass: 1948.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-SR / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.6 Å3/Da / Density % sol: 23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MgCl2 20mM, SrCl2 80mM, CaCl2 40mM, SPM 4Cl 12mM, Sodium cacodylate 20mM, 35% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 0.88→37.08 Å / Num. all: 19031 / Num. obs: 19031 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 0.88→0.93 Å / % possible all: 58.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 12.663 Å2
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Refinement step | Cycle: LAST / Resolution: 0.88→37.08 Å
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Refine LS restraints |
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