5V2R
Structure of a GA Rich 8x8 Nucleotide RNA Internal Loop
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 3.1 mM None RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3') | 95% H2O/5% D2O | 0.1 M | 6.2 | ambient | 273 | Varian INOVA 600 |
| 2 | 2D 1H-1H TOCSY | 3.1 mM None RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3') | 95% H2O/5% D2O | 0.1 M | 6.2 | ambient | 273 | Varian INOVA 600 |
| 3 | 2D 1H-1H NOESY | 3.1 mM None RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3') | 100% D2O | 0.1 M | 6.2 | ambient | 283 | Varian INOVA 600 |
| 4 | 2D 1H-1H TOCSY | 3.1 mM None RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3') | 100% D2O | 0.1 M | 6.2 | ambient | 283 | Varian INOVA 600 |
| 5 | 2D 31P-1H COSY | 3.1 mM None RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3') | 100% D2O | 0.1 M | 6.2 | ambient | 283 | Varian INOVA 600 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | Amber | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest restraint energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 33 |
| Representative Model | 1 (lowest restraint 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 | processing | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 4 | chemical shift assignment | Sparky | Goddard | |
| 5 | data analysis | Sparky | Goddard | |
| 6 | refinement | Amber | 14 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |
| 7 | data analysis | Amber | 14 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |
| 8 | structure calculation | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
