Solution structure of the HIV-1 PBS-segment
SOLUTION NMR - SOLUTION SCATTERING
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 250 uM 1H RNA (103-MER) | 100% D2O | 3 mM | 7.5 | 1 atm | 308 | Bruker AVANCE 800 |
| 2 | 2D 1H-1H NOESY | 250 uM A-8D, C-D, G-H, U-5,6-D2 RNA (103-MER) | 100% D2O | 3 mM | 7.5 | 1 atm | 308 | Bruker AVANCE 800 |
| 3 | 2D 1H-1H NOESY | 250 uM A-8D, C-D, G-8D, U-H RNA (103-MER) | 100% D2O | 3 mM | 7.5 | 1 atm | 308 | Bruker AVANCE 800 |
| 4 | 2D 1H-1H NOESY | 250 uM A-8D, C-5,6-D2, G-D, U-5,6-D2 RNA (103-MER) | 100% D2O | 3 mM | 7.5 | 1 atm | 308 | Bruker AVANCE 800 |
| 5 | 2D 1H-1H NOESY | 250 uM A-8D, C-D, G-8D, U-D RNA (103-MER) | 100% D2O | 3 mM | 7.5 | 1 atm | 308 | Bruker AVANCE 800 |
| 6 | 2D 1H-1H NOESY | 250 uM A-H, C-D, G-H, U-D RNA (103-MER) | 100% D2O | 3 mM | 7.5 | 1 atm | 308 | Bruker AVANCE 800 |
| 7 | 2D 1H-1H NOESY | 250 uM A-H, C-H, G-D, U-D RNA (103-MER) | 100% D2O | 3 mM | 7.5 | 1 atm | 308 | Bruker AVANCE 800 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics | Structure minimization | Amber |
| distance geometry | The SAXS scattering profiles for each structure were back calculated and the structures with lowest chi2 compared with experimental SAXS data were selected. | X-PLOR NIH |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | target function |
| Conformers Calculated Total Number | 1200 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 5 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 6 | processing | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 7 | chemical shift assignment | NMRView | Johnson, One Moon Scientific | |
| 8 | peak picking | NMRView | Johnson, One Moon Scientific | |
| 1 | structure calculation | CYANA | Guntert, Mumenthaler and Wuthrich | |
| 9 | geometry optimization | CYANA | Guntert, Mumenthaler and Wuthrich | |
| 4 | refinement | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman | |
| 2 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
