5VH8
Structure and dynamics of RNA repeat expansions that cause Huntington's Disease and myotonic dystrophy type 1
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 | 0.5 mM NA Adenosine, Cytidine,Guanosine, Uridine RNA (5'-R(*GP*AP*CP*CP*UP*GP*CP*UP*GP*CP*UP*GP*GP*UP*C)-3'), 5.0 mM potassium phosphate, 0.25 mM EDTA | 100% D2O | 0.0112 M | 6 | 1 atm | 298 | Bruker Avance III HD UltraShield 700 |
2 | 2D 1H-1H NOESY | 0.5 uM NA Adenosine, Cytidine,Guanosine, Uridine RNA (5'-R(*GP*AP*CP*CP*UP*GP*CP*UP*GP*CP*UP*GP*GP*UP*C)-3'), 5.0 mM potassium phosphate, 0.25 nM EDTA | 90% H2O/10% D2O | 0.0112 M | 6 | 1 atm | 276 | Bruker Avance III HD Ascend 850 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | Avance III HD UltraShield | 700 |
2 | Bruker | Avance III HD Ascend | 850 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 40 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | TopSpin | 3.5 | Bruker Biospin |
2 | refinement | Amber | 16 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |
3 | chemical shift assignment | Sparky | 3.0 | Goddard |
4 | peak picking | Sparky | 3.0 | Goddard |
5 | data analysis | Amber | 16 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |
6 | processing | NMRPipe | 8.9 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
7 | structure calculation | Amber | 16 |