2LI9
Metal binding domain of rat beta-amyloid
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-13C HSQC | 5 mM protein_1, 8 mM Zinc cloride, 20 mM [U-100% 2H] TRIS, 0.1 % sodium azide | 100% D2O | 10 | 7.1 | ambient | 278 | |
| 2 | 2D DQF-COSY | 5 mM protein_1, 8 mM Zinc cloride, 20 mM [U-100% 2H] TRIS, 0.1 % sodium azide | 90% H2O/10% D2O | 10 | 7.1 | ambient | 278 | |
| 3 | 2D DQF-COSY | 5 mM protein_1, 8 mM Zinc cloride, 20 mM [U-100% 2H] TRIS, 0.1 % sodium azide | 100% D2O | 10 | 7.1 | ambient | 278 | |
| 4 | 2D 1H-1H NOESY | 5 mM protein_1, 8 mM Zinc cloride, 20 mM [U-100% 2H] TRIS, 0.1 % sodium azide | 90% H2O/10% D2O | 10 | 7.1 | ambient | 278 | |
| 5 | 2D 1H-1H NOESY | 5 mM protein_1, 8 mM Zinc cloride, 20 mM [U-100% 2H] TRIS, 0.1 % sodium azide | 100% D2O | 10 | 7.1 | ambient | 278 | |
| 6 | 2D 1H-1H TOCSY | 5 mM protein_1, 8 mM Zinc cloride, 20 mM [U-100% 2H] TRIS, 0.1 % sodium azide | 100% D2O | 10 | 7.1 | ambient | 278 | |
| 7 | 2D 1H-1H TOCSY | 5 mM protein_1, 8 mM Zinc cloride, 20 mM [U-100% 2H] TRIS, 0.1 % sodium azide | 90% H2O/10% D2O | 10 | 7.1 | ambient | 278 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | Avance | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing, QM/MM geometry optimization | simulation in explicit water environment | TOPSPIN |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 40 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (closest to the average) |
| 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 | SPARKY | Goddard | |
| 4 | data analysis | AngleSearch | V. Polshakov | |
| 5 | structure solution | GROMACS | 3.3.1 | Van Der Spoel et al. |
| 6 | geometry optimization | GROMACS/CPMD | Biswas & Gogonea | |
| 7 | data analysis | ProcheckNMR | Laskowski and MacArthur | |
| 8 | data analysis | InsightII | Accelrys Software Inc. | |
| 9 | refinement | GROMACS | Van Der Spoel et al. | |
| 10 | refinement | GROMACS/CPMD | Biswas & Gogonea | |
