SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | 0.005 M DNA, 0.0001 M EDTA-d12, 0.050 M Thallium-Nitrate, pH 6.0 | 100% D2O | 6.5 | 1 atm | 298 | ||
| 2 | DQF-COSY | 0.005 M DNA, 0.0001 M EDTA-d12, 0.050 M Thallium-Nitrate, pH 6.0 | 100% D2O | 6.5 | 1 atm | 298 | ||
| 3 | 31P-1H COSY | 0.005 M DNA, 0.0001 M EDTA-d12, 0.050 M Thallium-Nitrate, pH 6.0 | 100% D2O | 6.5 | 1 atm | 298 | ||
| 4 | 2D NOESY | 0.005 M DNA, 0.0001 M EDTA-d12, 0.050 M Thallium-Nitrate, pH 6.0 | 90% H2O/10% D2O | 6.5 | 1 atm | 278 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | UNITYPLUS | 600 |
| 2 | Varian | INOVA | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| (1) distance geometry with simulated annealing; (2) torsion angle dynamics (2000 K for 60 ps with 15 fs timesteps); (3) cartesian dynamics (1000 K for 5 ps with 5 fs timesteps); (4) restrained molecular dynamics (100 cycles of 200 steps each) | VNMR | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (closest to the average) |
| Additional NMR Experimental Information | |
|---|---|
| Details | This structure was determined without the use of isotopically enriched nucleotides. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | VNMR | 6.1b | Varian, Inc |
| 2 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer, Bax | |
| 3 | data analysis | Sparky | 3.110 | Goddard and Kneller |
| 4 | iterative matrix relaxation | CNS | 1.1 | Brunger, Adams, Clore, Delano, Gros, Grosse-Kunstleve, Jiang, Kuszewski, Nilges, Pannu, Read, Rice, Simonson, Warren |
| 5 | refinement | CNS | 1.1 | Brunger, Adams, Clore, Delano, Gros, Grosse-Kunstleve, Jiang, Kuszewski, Nilges, Pannu, Read, Rice, Simonson, Warren |
| 6 | structure solution | CNS | 1.1 | Brunger, Adams, Clore, Delano, Gros, Grosse-Kunstleve, Jiang, Kuszewski, Nilges, Pannu, Read, Rice, Simonson, Warren |
