Structure of the transcription regulator SvtR from the hyperthermophilic archaeal virus SIRV1
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 1.6 mM svtR, 20 mM [U-2H] sodium acetate | 90% H2O/10% D2O | 0.0004 | 5.5 | ambient | 298 | |
| 2 | 2D 1H-1H NOESY | 1.2 mM svtR, 20 mM [U-2H] sodium acetate | 100% D2O | 0.0004 | 5.5 | ambient | 298 | |
| 3 | 3D 1H-13C NOESY | 1.5 mM [U-98% 13C; U-98% 15N] svtR, 20 mM [U-2H] sodium acetate | 88% H2O/12% D2O | 0.0004 | 5.5 | ambient | 298 | |
| 4 | 3D DOUBLY-FILTERED 1H-13C NOESY | 2.9 mM 50%[U-98% 13C; U-98% 15N]; 50% natural abundance svtR, 20 mM [U-2H] sodium acetate | 88% H2O/12% D2O | 0.0004 | 5.5 | ambient | 298 | |
| 5 | 3D 1H-15N NOESY | 1.7 mM [U-98% 15N] svtR, 20 mM [U-2H] sodium acetate | 90% H2O/10% D2O | 0.0004 | 5.5 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 600 |
| 2 | Varian | INOVA | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | Residues 1-12 are disordered. Only coordinates for residues 11-56 are included. Structures were calculated with restraints for residues 11-56. | ARIA |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 200 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | structure solution | ARIA | 2.2 | Linge, O'Donoghue and Nilges |
| 2 | noe assignment | ARIA | 2.2 | Linge, O'Donoghue and Nilges |
| 3 | structure solution | CNS | 1.1 | Brunger, Adams, Clore, Gros, Nilges and Read |
| 4 | refinement | CNS | 1.1 | Brunger, Adams, Clore, Gros, Nilges and Read |
| 5 | collection | VnmrJ | 2.1B | Varian |
| 6 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 7 | data analysis | NMRView | 5.2.2 | Johnson, One Moon Scientific |
| 8 | chemical shift assignment | NMRView | 5.2.2 | Johnson, One Moon Scientific |
| 9 | peak picking | NMRView | 5.2.2 | Johnson, One Moon Scientific |
| 10 | data analysis | ProcheckNMR | 3.4 | Laskowski and MacArthur |
| 11 | data analysis | WHAT IF | Vriend | |
