6N8I
RNA Duplex containing the internal loop 5'-UUCG/3'-GCUU
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 | 1 mM RNA (5'-R(*CP*GP*CP*AP*UP*UP*CP*GP*AP*CP*GP*C)-3'), 1 mM RNA (5'-R(*GP*CP*GP*UP*UP*UP*CP*GP*UP*GP*CP*G)-3') | 90% H2O/10% D2O | 130 Na+ mM | 6.2 | 1 atm | 293 | Varian INOVA 600 |
2 | 2D 1H-1H TOCSY | 1 mM RNA (5'-R(*CP*GP*CP*AP*UP*UP*CP*GP*AP*CP*GP*C)-3'), 1 mM RNA (5'-R(*GP*CP*GP*UP*UP*UP*CP*GP*UP*GP*CP*G)-3') | 90% H2O/10% D2O | 130 Na+ mM | 6.2 | 1 atm | 293 | Varian INOVA 600 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (closest to the average) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | refinement | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
2 | structure calculation | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
3 | chemical shift assignment | Sparky | Goddard | |
4 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
6 | data analysis | Sparky | Goddard | |
5 | processing | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |