Average solution structure of a pseudo-5'-splice site from the negative regulator of splicing of Rous Sarcoma virus
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | RNA Residues 907-929 from NRS (NRS23) | 10 mM Sodium Phosphate, 25 mM NaCl, pH 6.5 | 25 mM NaCl, 10 mM NaPi | 6.5 | ambient | 298 | |
| 2 | 3D_13C-separated_NOESY | RNA Residues 907-929 from NRS (NRS23) | 10 mM Sodium Phosphate, 25 mM NaCl, pH 6.5 | 25 mM NaCl, 10 mM NaPi | 6.5 | ambient | 298 | |
| 3 | HNN-COSY | RNA Residues 907-929 from NRS (NRS23) | 10 mM Sodium Phosphate, 25 mM NaCl, pH 6.5 | 25 mM NaCl, 10 mM NaPi | 6.5 | ambient | 298 | |
| 4 | DQF-COSY | RNA Residues 907-929 from NRS (NRS23) | 10 mM Sodium Phosphate, 25 mM NaCl, pH 6.5 | 25 mM NaCl, 10 mM NaPi | 6.5 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 500 |
| 2 | Varian | INOVA | 600 |
| 3 | Varian | INOVA | 800 |
| 4 | Bruker | DRX | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| Simulated annealing. Torsion angle dynamics in refinement. | 100 structurews were calculated, the minimized average from the 15 lowest energy structures is presented. Constraints used: 423 distance, 63 torsion angle, 117 orientation (RDC). The DELPIC database was employed in the refinement as follows: torsion angle database active for all residues, base-base positional database active for residues 907-912, 914-916, and 921-929. DELPHIC database reference: Clore, G.M. Kuszewski, J. J. Am. Chem. Soc. 125: 1518-1525 | Xplor-NIH |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | |
| Conformers Calculated Total Number | |
| Conformers Submitted Total Number | 1 |
| Representative Model | 1 (minimized average structure) |
| Additional NMR Experimental Information | |
|---|---|
| Details | Exchangeable proton spectra collected at 15 Celsius |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | Xplor-NIH | xplor-nih-2.0.6 | C.D. Schwieters, J.J. Kuszewski,N. Tjandra, and G.M. Clore |
| 2 | data analysis | NMRPipe | 4.1 | F. Delaglio, S. Grzesiek, G. Vuister, G. Zhu, J. Pfeifer, and A. Bax |
| 3 | collection | VNMR | 6.1C | varian inc. |
| 4 | data analysis | NMRView | 5.0.4 | Johnson, B.A. |
