2L9I
NMR structure of thymosin alpha-1
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 28.8 mg Thymosin-Alpha1, 40 % TFE | 10% D2O, 50% H2O | 0 | 4.9 | ambient | 298 | |
| 2 | 2D 1H-1H TOCSY | 28.8 mg Thymosin-Alpha1, 40 % TFE | 10% D2O, 50% H2O | 0 | 4.9 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | UNITYPLUS | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics, restrained molecular dynamics, restrained molecular dynamics and selection, average structure | 25 ns at 300K on a explicit solvent ratio 40% TFE/H2O (v/v), with a linear-helix initial structure, After the 25 ns on explicit solvent, 1 ns GB simulation follows with all (549)restrains at 300K., After the 1ns GB restrained simulation, a 10ns restrained MD simulation follows on a explicit solvent ratio 40% TFE/water (v/v). 1000 structures were collected (1 every 10ps), minimized and sorted by total energy. The best 20 structures with the lowest energy were selected., The average structure was obtained from the average of the 20 best structures with the lowest energy and minimized with the 549 restraints and the GB method in order to taking in account the salvation implicitly. | AMBER |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | 1 average structure + 20 structures with the lowest energy |
| Conformers Calculated Total Number | 1000 |
| Conformers Submitted Total Number | 21 |
| Representative Model | 1 (average structure) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | molecular dynamics | AMBER | 9.0 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm |
| 2 | minimization | AMBER | 9.0 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm |
| 3 | data analysis | AMBER | 9.0 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm |
| 4 | refinement | AMBER | ||
