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Open data
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Basic information
Entry | Database: PDB / ID: 7efg | ||||||||||||||||||||||||||||
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Title | RNA kink-turn motif | ||||||||||||||||||||||||||||
![]() | RNA (5'-R(*![]() ![]() Function / homology | ![]() ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Kondo, J. / Nagashima, M. | Funding support | 1items |
![]() ![]() Title: RNA kink-turn motif Authors: Kondo, J. / Nagashima, 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 | ![]() | 21 KB | Display | ![]() |
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PDB format | ![]() | 11.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7efhC ![]() 4cs1S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: RNA chain | Mass: 6233.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.77 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: sodium cacodylate, MPD, spermine tetrahydrochloride, sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.6→37.53 Å / Num. obs: 2386 / % possible obs: 99.9 % / Redundancy: 33.53 % / Biso Wilson estimate: 41.88 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 55.91 |
Reflection shell | Resolution: 2.6→2.66 Å / Redundancy: 33.54 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 15.98 / Num. unique obs: 177 / % possible all: 99.4 |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: 4CS1 Resolution: 2.6→37.53 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 18.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||
Displacement parameters | Biso mean: 38.65 Å2 | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→37.53 Å
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LS refinement shell |
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