6T2G
NMR structure of KRAS32R G25T conformer G-quadruplex within KRAS promoter region
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 KRAS32R G25T no labelled | 90% H2O/10% D2O | 50 KCl ; 10 KPi mM | 6.66 | 1 atm | 310 | Bruker AVANCE III 850 |
2 | 2D 1H-15N HSQC | 0.5 mM [U-99% 13C; U-99% 15N] KRAS32R G25T | 90% H2O/10% D2O | 50 KCl ; 10 KPi mM | 6.66 | 1 atm | 310 | Bruker AVANCE III 850 |
3 | 2D 1H-13C HSQC aromatic | 0.5 mM [U-99% 13C; U-99% 15N] KRAS32R G25T | 90% H2O/10% D2O | 50 KCl ; 10 KPi mM | 6.66 | 1 atm | 310 | Bruker AVANCE III 850 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE III | 700 |
2 | Bruker | AVANCE III | 850 |
NMR Refinement | ||
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Method | Details | Software |
molecular dynamics | Amber |
NMR Ensemble Information | |
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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 | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | Amber | 12 | 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 |