7BLM
AG repetition attached to a compact i-motif clip at 3'-end
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 1.3 mM AGAGCCC | 90% H2O/10% D2O | 60 mM | 5 | 1 atm | 278 | Bruker AVANCE III HD 700 |
| 2 | 2D 1H-1H NOESY | 1.3 mM AGAGCCC | 100% D2O | 60 mM | 5 | 1 atm | 288 | Bruker AVANCE III HD 700 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE III HD | 700 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics | In total, 1 microsecond of unrestrained MD in explicit solvent. Trajectory after 300 ns discarded due to partial disruption of NMR-derived structure. | Amber |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | Snapshot every 100 nanoseconds taken from initial 300 ns of 1 microsecond unrestrained MD. |
| Conformers Calculated Total Number | 3000 |
| Conformers Submitted Total Number | 4 |
| Representative Model | 1 (minimized average structure) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | Amber | 16 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |
| 2 | structure calculation | Amber | 16 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |
| 3 | chemical shift assignment | NMRFAM-SPARKY | 1.413 | Nuclear Magnetic Resonance Facility at Madison |
| 4 | collection | TopSpin | 4 | Bruker Biospin |
