Solution structures of second bromodomain of Brd4 with di-acetylated Twist peptide
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D HNCACB | 5 mM [U-100% 2H] DTT, 100 mM sodium phosphate | 90% H2O/10% D2O | 6.5 | ambient | 298 | ||
| 2 | 3D HN(COCA)CB | 5 mM [U-100% 2H] DTT, 100 mM sodium phosphate | 90% H2O/10% D2O | 6.5 | ambient | 298 | ||
| 3 | 3D 1H-15N NOESY | 5 mM [U-100% 2H] DTT, 100 mM sodium phosphate | 90% H2O/10% D2O | 6.5 | ambient | 298 | ||
| 4 | 3D 1H-15N TOCSY | 5 mM [U-100% 2H] DTT, 100 mM sodium phosphate | 90% H2O/10% D2O | 6.5 | ambient | 298 | ||
| 5 | 3D 1H-13C NOESY aliphatic | 5 mM [U-100% 2H] DTT, 100 mM sodium phosphate | 100% D2O | 6.5 | ambient | 298 | ||
| 6 | 3D 1H-13C NOESY aromatic | 5 mM [U-100% 2H] DTT, 100 mM sodium phosphate | 100% D2O | 6.5 | ambient | 298 | ||
| 7 | 3D 13C-edited 13C/15N-filtered NOESY aromatic | 5 mM [U-100% 2H] DTT, 100 mM sodium phosphate | 100% D2O | 6.5 | ambient | 298 | ||
| 8 | 3D 13C-edited 13C/15N-filtered NOESY aliphatic | 5 mM [U-100% 2H] DTT, 100 mM sodium phosphate | 100% D2O | 6.5 | ambient | 298 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 900 |
| 2 | Bruker | AVANCE | 800 |
| 3 | Bruker | AVANCE | 700 |
| 4 | Bruker | AVANCE | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing, DGSA-distance geometry simulated annealing | ARIA | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 200 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | ARIA | 2.2 | Linge, O'Donoghue and Nilges |
| 2 | chemical shift calculation | NMRPipe | 7.1 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
| 3 | processing | NMRPipe | 7.1 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
| 4 | peak picking | NMRView | 5.04 | Johnson, One Moon Scientific |
| 5 | data analysis | NMRView | 5.04 | Johnson, One Moon Scientific |
| 6 | chemical shift assignment | NMRView | 5.04 | Johnson, One Moon Scientific |
| 7 | structure solution | CNS | 1.2 | Brunger, Adams, Clore, Gros, Nilges and Read |
| 8 | geometry optimization | CNS | 1.2 | Brunger, Adams, Clore, Gros, Nilges and Read |
| 9 | collection | TopSpin | 1.3 | Bruker Biospin |
| 10 | refinement | CNS | Brunger, Adams, Clore, Gros, Nilges and Read | |
