SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 2 mM RKEC1 DNA (27-MER), 2.25 mM L-DOPAMINE, 20 mM sodium phosphate, 140 mM sodium chloride, 2 mM magnesium chloride | 90% H2O/10% D2O | 162 mM | 7.4 | 1 atm | 278 | Bruker AVANCE NEO 800 |
| 2 | 2D 1H-1H NOESY | 2 mM RKEC1 DNA (27-MER), 2.25 mM L-DOPAMINE, 20 mM sodium phosphate, 140 mM sodium chloride, 2 mM magnesium chloride | 100% D2O | 162 mM | 7.4 | 1 atm | 298 | Bruker AVANCE NEO 800 |
| 3 | 2D 1H-1H TOCSY | 2 mM RKEC1 DNA (27-MER), 2.25 mM L-DOPAMINE, 20 mM sodium phosphate, 140 mM sodium chloride, 2 mM magnesium chloride | 100% D2O | 162 mM | 7.4 | 1 atm | 298 | Bruker AVANCE NEO 800 |
| 4 | 2D DQF-COSY | 2 mM RKEC1 DNA (27-MER), 2.25 mM L-DOPAMINE, 20 mM sodium phosphate, 140 mM sodium chloride, 2 mM magnesium chloride | 100% D2O | 162 mM | 7.4 | 1 atm | 298 | Bruker AVANCE NEO 800 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE NEO | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | Note that the deposited ambig.tbl, unambig.tbl and dihedrals.tbl were used with ARIA/CNS | NMRPipe |
| simulated annealing | note that H5' and H5'' were freely swapped during this step | CNS |
| molecular dynamics | Note that the final refinement with AMBER, and therefore the deposited ensemble, only used the unambig.tbl restraints | Amber |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 15 |
| Representative Model | 1 (closest to the average) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | chemical shift assignment | NMRFAM-SPARKY | 1.470 | Lee, Tonelli and Markley |
| 2 | structure calculation | CNS | 1.2 | Brunger, Adams, Clore, Gros, Nilges and Read |
| 3 | refinement | Amber | 24 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |
| 4 | structure calculation | ARIA | 2.3 | Linge, O'Donoghue and Nilges |
| 5 | peak picking | NMRFAM-SPARKY | 1.470 | Lee, Tonelli and Markley |
| 6 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
