NMR-driven structure of the KRAS4B-G12D "alpha-alpha" dimer on a lipid bilayer nanodisc
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-13C TROSY | 80 uM ILV 13C-methyl; Lys 15N-amide KRAS4B | 90% H2O/10% D2O | 100 mM | 7.4 | 1 atm | 288 | Bruker AVANCE III 800 |
| 2 | 2D 1H-15N HSQC | 80 uM ILV 13C-methyl; Lys 15N-amide KRAS4B | 90% H2O/10% D2O | 100 mM | 7.4 | 1 atm | 288 | Bruker AVANCE III 800 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE III | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | PDB entry 4DSO was refined and then used the build the model for GTPase KRas. | HADDOCK |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 1000 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | TopSpin | Bruker Biospin | |
| 2 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 3 | data analysis | NMRView | Johnson, One Moon Scientific | |
| 4 | refinement | HADDOCK | Bonvin | |
| 5 | structure calculation | HADDOCK | Bonvin | |
