Major Conformation of the Internal Loop 5'GGAGUC/3'CUGAGG
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 2.0 mM 5'-GAGGAGUCUCA-3', 70 mM NaCl, 30 mM NaH2PO4/Na2HPO4, 0.1 mM EDTA | 95% H2O/5% D2O | 100 mM | 6.1 | 1 atm | 274 | Varian UNITY INOVA 600 |
| 2 | 2D 1H-1H TOCSY | 2.0 mM 5'-GAGGAGUCUCA-3', 70 mM NaCl, 30 mM NaH2PO4/Na2HPO4, 0.1 mM EDTA | 95% H2O/5% D2O | 100 mM | 6.1 | 1 atm | 274 | Varian UNITY INOVA 600 |
| 3 | 2D 1H-13C HSQC | 2.0 mM 5'-GAGGAGUCUCA-3', 70 mM NaCl, 30 mM NaH2PO4/Na2HPO4, 0.1 mM EDTA | 95% H2O/5% D2O | 100 mM | 6.1 | 1 atm | 274 | Varian UNITY INOVA 600 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | UNITY INOVA | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | 24 distance restraints from hydrogen bonds, 132 dihedral angle restraints | Amber |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest constraint energy |
| Conformers Calculated Total Number | 600 |
| Conformers Submitted Total Number | 30 |
| Representative Model | 1 (lowest constraint energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | VNMR | 6.1C | Varian |
| 2 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 3 | chemical shift assignment | NMRFAM-SPARKY | 1.2 | Lee, Tonelli, Markley |
| 4 | peak picking | NMRFAM-SPARKY | 1.2 | Lee, Tonelli, Markley |
| 5 | refinement | Amber | v16 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman |
| 6 | structure calculation | Amber | v16 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman |
