SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N HSQC | 0.5 mM [U-100% 15N] ING4 PHD mutant N214D, 30 uM DSS, 1 mM DTT, 20 mM sodium phosphate, 50 mM sodium chloride | 90% H2O/10% D2O | 70 | 6.5 | 1 atm | 298 | |
| 2 | 2D 1H-1H NOESY | 0.5 mM [U-100% 15N] ING4 PHD mutant N214D, 30 uM DSS, 1 mM DTT, 20 mM sodium phosphate, 50 mM sodium chloride | 90% H2O/10% D2O | 70 | 6.5 | 1 atm | 298 | |
| 3 | 3D 1H-15N NOESY | 0.5 mM [U-100% 15N] ING4 PHD mutant N214D, 30 uM DSS, 1 mM DTT, 20 mM sodium phosphate, 50 mM sodium chloride | 90% H2O/10% D2O | 70 | 6.5 | 1 atm | 298 | |
| 4 | 3D 1H-15N TOCSY | 0.5 mM [U-100% 15N] ING4 PHD mutant N214D, 30 uM DSS, 1 mM DTT, 20 mM sodium phosphate, 50 mM sodium chloride | 90% H2O/10% D2O | 70 | 6.5 | 1 atm | 298 | |
| 5 | 2D 1H-1H TOCSY | 0.5 mM [U-100% 15N] ING4 PHD mutant N214D, 30 uM DSS, 1 mM DTT, 20 mM sodium phosphate, 50 mM sodium chloride | 90% H2O/10% D2O | 70 | 6.5 | 1 atm | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 600 |
| 2 | Bruker | AVANCE | 700 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| torsion angle dynamics, molecular dynamics | Simulated annealing combined with torsion angle dynamics. Iterative cycles of structure calculation and NOE assignment. Energy minimization in vacuo with implicit solvent (distance dependent dielecric constant) | XwinNMR |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | target function |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 25 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | XwinNMR | Bruker | |
| 2 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 3 | data analysis | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 4 | data analysis | NMRView | Johnson, One Moon Scientific | |
| 5 | chemical shift assignment | NMRView | Johnson, One Moon Scientific | |
| 6 | peak picking | NMRView | Johnson, One Moon Scientific | |
| 7 | structure solution | CYANA | Guntert, Mumenthaler and Wuthrich | |
| 8 | refinement | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo and Kollman | |
| 9 | refinement | CYANA | Guntert, Mumenthaler and Wuthrich | |
