7QA9
10bp DNA/DNA duplex
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 0.4 mM no DNA (5'-D(*CP*CP*AP*TP*TP*AP*TP*AP*GP*C)-3'), 0.4 mM no DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*TP*GP*G)-3'), 10 mM no sodium phosphate | 100% D2O | 10 mM | 7.0 | 1 atm | 278 | Bruker AVANCE NEO 600 |
2 | 2D NOESY | 0.4 mM no DNA (5'-D(*CP*CP*AP*TP*TP*AP*TP*AP*GP*C)-3'), 0.4 mM no DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*TP*GP*G)-3'), 10 mM no sodium phosphate | 90% H2O/10% D2O | 10 mM | 7.0 | 1 atm | 278 | Bruker AVANCE NEO 600 |
3 | 2D DQF-COSY | 0.4 mM no DNA (5'-D(*CP*CP*AP*TP*TP*AP*TP*AP*GP*C)-3'), 0.4 mM no DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*TP*GP*G)-3'), 10 mM no sodium phosphate | 100% D2O | 10 mM | 7.0 | 1 atm | 278 | Bruker AVANCE NEO 600 |
4 | 2D 1H-1H TOCSY | 0.4 mM no DNA (5'-D(*CP*CP*AP*TP*TP*AP*TP*AP*GP*C)-3'), 0.4 mM no DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*TP*GP*G)-3'), 10 mM no sodium phosphate | 100% D2O | 10 mM | 7.0 | 1 atm | 278 | Bruker AVANCE NEO 600 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE NEO | 600 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing | Amber |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 50 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | collection | TopSpin | Bruker Biospin | |
2 | chemical shift assignment | TopSpin | Bruker Biospin | |
3 | chemical shift assignment | NMRFAM-SPARKY | Lee W, Tonelli M, Markley JL | |
4 | peak picking | NMRFAM-SPARKY | Lee W, Tonelli M, Markley JL | |
5 | structure calculation | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |