6T51
NMR structure of KRAS22RT G-quadruplex forming within KRAS promoter region at physological temperature
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 2 mM KRAS22RT | 90% H2O/10% D2O | 50 KCl; 10KPi mM | 6.66 | 1 atm | 310 | Bruker AVANCE III 950 |
2 | 2D 1H-13C HSQC | 0.5 mM [U-99% 13C; U-99% 15N] KRAS22RT | 90% H2O/10% D2O | 50 KCl; 10KPi mM | 6.66 | 1 atm | 310 | Bruker AVANCE III 800 |
3 | 2D 1H-15N HSQC | 0.5 mM [U-99% 13C; U-99% 15N] KRAS22RT | 90% H2O/10% D2O | 50 KCl; 10KPi mM | 6.66 | 1 atm | 310 | Bruker AVANCE III 950 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE III | 950 |
2 | Bruker | AVANCE III | 800 |
3 | Bruker | AVANCE III | 700 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
molecular dynamics | Amber |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 750 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | refinement | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
2 | structure calculation | ARIA | Linge, O'Donoghue and Nilges | |
3 | chemical shift assignment | Sparky | Goddard | |
4 | processing | TopSpin | Bruker Biospin | |
5 | peak picking | CcpNmr Analysis | CCPN |