2MR9
NMR structure of UBA domain of DNA-damage-inducible 1 protein (Ddi1)
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N HSQC | 1 mM [U-100% 15N] UBA, 7 % [U-99% 2H] D2O, 93 % H2O, 20 mM sodium phosphate | 93% H2O/7% D2O | 10 | 6.8 | ambient atm | 298.2 | |
| 2 | 2D 1H-1H TOCSY | 1 mM [U-100% 15N] UBA, 7 % [U-99% 2H] D2O, 93 % H2O, 20 mM sodium phosphate | 93% H2O/7% D2O | 10 | 6.8 | ambient atm | 298.2 | |
| 3 | 2D 1H-1H NOESY | 1 mM [U-100% 15N] UBA, 7 % [U-99% 2H] D2O, 93 % H2O, 20 mM sodium phosphate | 93% H2O/7% D2O | 10 | 6.8 | ambient atm | 298.2 | |
| 4 | 3D 1H-15N NOESY | 1 mM [U-100% 15N] UBA, 7 % [U-99% 2H] D2O, 93 % H2O, 20 mM sodium phosphate | 93% H2O/7% D2O | 10 | 6.8 | ambient atm | 298.2 | |
| 5 | 3D 1H-15N TOCSY | 1 mM [U-100% 15N] UBA, 7 % [U-99% 2H] D2O, 93 % H2O, 20 mM sodium phosphate | 93% H2O/7% D2O | 10 | 6.8 | ambient atm | 298.2 | |
| 6 | RDC | 0.5 mM [U-100% 15N] UBA, 7 % [U-99% 2H] D2O, 43 % H2O, 10 mM sodium phosphate, 5 % C12E5, 45 % n-hexanol | 93% H2O/7% D2O | 10 | 6.8 | ambient atm | 298.2 | |
| 7 | RDC | 0.5 mM [U-100% 15N] UBA, 7 % [U-99% 2H] D2O, 43 % H2O, 10 mM sodium phosphate, 5 % C12E5, 45 % n-hexanol | 93% H2O/7% D2O | 10 | 6.8 | ambient atm | 308.2 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | CARA | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 10 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | peak picking | CARA | 1.8.1 | Keller and Wuthrich |
| 2 | chemical shift assignment | CARA | 1.8.1 | Keller and Wuthrich |
| 3 | collection | TopSpin | 2.1 | Bruker Biospin |
| 4 | processing | TopSpin | 2.1 | Bruker Biospin |
| 5 | data analysis | TopSpin | 2.1 | Bruker Biospin |
| 6 | chemical shift calculation | ARIA | 2.1 | Linge, O'Donoghue and Nilges |
| 7 | structure solution | ARIA | 2.1 | Linge, O'Donoghue and Nilges |
| 8 | refinement | ARIA | 2.1 | Linge, O'Donoghue and Nilges |
