NMR solution structure of tRNA-Arg-UCU-4-1 anticodon stem loop with no chemical modifications
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 10 mM sodium phosphate, 300 uM tRNA-Arg-UCU-4-1 Anticodon stem-loop, 50 uM EDTA | 90% H2O/10% D2O | 10 mM | 6.3 | 1 atm | 288 | Bruker AVANCE III 800 |
| 2 | 2D 1H-1H TOCSY | 10 mM sodium phosphate, 300 uM tRNA-Arg-UCU-4-1 Anticodon stem-loop, 50 uM EDTA | 90% H2O/10% D2O | 10 mM | 6.3 | 1 atm | 288 | Bruker AVANCE III 800 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE III | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | Amber | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the least restraint violations |
| Conformers Calculated Total Number | 300 |
| Conformers Submitted Total Number | 15 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 4 | collection | TopSpin | Bruker Biospin | |
| 5 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 1 | chemical shift assignment | NMRFAM-SPARKY | University of Madison-Wisconsin | |
| 2 | structure calculation | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman | |
| 3 | refinement | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman | |
