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Open data
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Basic information
Entry | Database: PDB / ID: 1j9h | ||||||||||||||||||
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Title | Crystal Structure of an RNA Duplex with Uridine Bulges | ||||||||||||||||||
![]() | 5'-R(*![]() RNA / Uridine Bulge / RNA duplex / A-form / Kink / Metal binding | Function / homology | RNA | ![]() Method | ![]() ![]() ![]() ![]() Xiong, Y. / Deng, J. / Sudarsanakumar, C. / Sundaralingam, M. | ![]() ![]() Title: Crystal structure of an RNA duplex r(gugucgcac)(2) with uridine bulges. Authors: Xiong, Y. / Deng, J. / Sudarsanakumar, C. / Sundaralingam, M. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 34.4 KB | Display | ![]() |
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PDB format | ![]() | 23.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 350.4 KB | Display | ![]() |
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Full document | ![]() | 350.4 KB | Display | |
Data in XML | ![]() | 1.8 KB | Display | |
Data in CIF | ![]() | 3.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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
#1: RNA chain | Mass: 2910.639 Da / Num. of mol.: 4 / Source method: obtained synthetically #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.09 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6 Details: 20mM sodium cacodylate (pH 6.0), 10mM calcium chloride, 100mM sodium chloride, and 10%(v/v) MPD against 50% MPD in the reservoir, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 293 K | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. obs: 33934 / % possible obs: 99.3 % / Redundancy: 9 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 22 |
Reflection | *PLUS Lowest resolution: 20 Å |
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Processing
Software |
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.212 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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