6MCI
Solution structure of 7SK stem-loop 1
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 0.5 mM 7SK RNA, 10mM Phosphate, 70mM NaCl, 0.1mM EDTA, 90%H2O/10%D2O | 90% H2O/10% D2O | 10mM Phosphate, 70mM NaCl mM | 5.4 | 100000 Pa | 283 | Bruker DMX 700 |
2 | 2D 1H-15N HSQC | 0.5 mM [U-13C; U-15N] 7SK RNA, 10mM Phosphate, 70mM NaCl, 0.1mM EDTA, 90%H2O/10%D2O | 90% H2O/10% D2O | 10mM Phosphate, 70mM NaCl mM | 5.4 | 100000 Pa | 283 | Bruker DMX 700 |
3 | 2D 1H-13C HSQC | 0.5 mM [U-13C; U-15N] 7SK RNA, 10mM Phosphate, 70mM NaCl, 0.1mM EDTA | 100% D2O | 10mM Phosphate, 70mM NaCl mM | 5.4 | 100000 Pa | 283 | Bruker DMX 700 |
4 | 2D 1H-1H NOESY | 0.5 mM 7SK RNA, 10mM Phosphate, 70mM NaCl, 0.1mM EDTA | 100% D2O | 10mM Phosphate, 70mM NaCl mM | 5.4 | 100000 Pa | 283 | Bruker DMX 700 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DMX | 700 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing | Amber |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | target function |
Conformers Calculated Total Number | 20 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (target function) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | collection | TopSpin | Bruker Biospin | |
2 | peak picking | NMRView | Johnson, One Moon Scientific | |
3 | chemical shift assignment | NMRView | Johnson, One Moon Scientific | |
4 | data analysis | CYANA | Guntert, Mumenthaler and Wuthrich | |
5 | processing | CYANA | Guntert, Mumenthaler and Wuthrich | |
6 | structure calculation | CYANA | Guntert, Mumenthaler and Wuthrich | |
7 | refinement | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman |