Dimer Initiation Sequence of HIV-1Lai Genomic RNA: NMR Solution Structure of the Extended Duplex
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | 2mM oligonucleotide, 10mM phosphate buffer 100 mM NaCl | 90% H2O/10% D2O | 100mM NaCl | 5.8 | ambient | 278 | |
| 2 | 2D NOESY | 2mM oligonucleotide, 10mM phosphate buffer, 100 mM NaCl | 100% D2O | 100mM NaCl | 5.8 | ambient | 288 | |
| 3 | DQF-COSY | 2mM oligonucleotide, 10mM phosphate buffer, 100 mM NaCl | 100% D2O | 100mM NaCl | 5.8 | ambient | 288 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AMX | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing, matrix relaxation | UXNMR | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy |
| Conformers Calculated Total Number | 15 |
| Conformers Submitted Total Number | 15 |
| Representative Model | 11 (lowest energy) |
| Additional NMR Experimental Information | |
|---|---|
| Details | This structure was determined using standard 2D homonuclear techniques |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | UXNMR | ||
| 2 | processing | UXNMR | ||
| 3 | structure solution | X-PLOR | 3.851 | Brunger |
| 4 | data analysis | Curves | 5.0 | Lavery |
| 5 | refinement | X-PLOR | 3.851 | Brunger |
