2KVJ
NMR and MD solution structure of a Gamma-Methylated PNA duplex
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | [dsPNA]=0.4 mM Peptide Nucleic Acid-1 | 10 mM sodium phosphate buffer | 17.6 | 7 | ambient | 300 | |
| 2 | 2D 1H-1H COSY | [dsPNA]=0.4 mM Peptide Nucleic Acid-1 | 10 mM sodium phosphate buffer | 17.6 | 7 | ambient | 300 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing, molecular dynamics | 2 ns restrained MD | Amber |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | model 1 is the average of 10 NMR-determined structures |
| Conformers Calculated Total Number | 11 |
| Conformers Submitted Total Number | 11 |
| Representative Model | 1 (minimized average structure) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | structure solution | Amber | 10 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollm |
| 2 | refinement | Amber | 10 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollm |
