2RP4
Solution Structure of the oligomerization domain in Dmp53
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N HSQC | 20mM sodium phosphate, 100mM sodium chloride, 0.03% sodium azide, 0.5-0.8mM [U-15N] protein | 90% H2O/10% D2O | 7 | ambient | 298 | ||
| 2 | 3D HNCA | 20mM sodium phosphate, 100mM sodium chloride, 0.03% sodium azide, 0.5-0.8mM [U-13C; U-15N] protein | 90% H2O/10% D2O | 7 | ambient | 298 | ||
| 3 | 3D 1H-15N NOESY | 20mM sodium phosphate, 100mM sodium chloride, 0.03% sodium azide, 0.5-0.8mM [U-15N] protein | 90% H2O/10% D2O | 7 | ambient | 298 | ||
| 4 | 3D 1H-13C NOESY | 20mM sodium phosphate, 100mM sodium chloride, 0.03% sodium azide, 0.5-0.8mM [U-13C; U-15N] protein | 90% H2O/10% D2O | 7 | ambient | 298 | ||
| 5 | 2D 1H-1H NOESY | 20mM sodium phosphate, 100mM sodium chloride, 0.5-0.8mM protein | 100% D2O | 7 | ambient | 298 | ||
| 6 | 4D J Resolved NOESY | 20mM sodium phosphate, 100mM sodium chloride, 0.5mM [U-13C; U-15N] protein | 100% D2O | 7 | ambient | 298 | ||
| 7 | 2D 1H-1H TOCSY | 20mM sodium phosphate, 100mM sodium chloride, 0.5-0.8mM protein | 100% D2O | 7 | ambient | 298 | ||
| 8 | 3D HN(CO)CA | 20mM sodium phosphate, 100mM sodium chloride, 0.03% sodium azide, 0.5-0.8mM [U-13C; U-15N] protein | 90% H2O/10% D2O | 7 | ambient | 298 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 700 |
| 2 | Bruker | AVANCE | 800 |
| 3 | Bruker | AVANCE | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | 100 structures were calculated with Aria1.2, then 20 lowest energies structures underwent water refinement | ARIA |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | chemical shift assignment | ARIA | 1.2 | Linge, O'Donoghue, Nilges |
| 2 | refinement | ARIA | 1.2 | Linge, O'Donoghue, Nilges |
| 3 | chemical shift assignment | XEASY | Bartels et al. | |
| 4 | geometry optimization | TALOS | Cornilescu, Delaglio, Bax | |
| 5 | collection | XwinNMR | Bruker Biospin | |
| 6 | processing | XwinNMR | Bruker Biospin | |
| 7 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer, Bax | |
