5V2R
Structure of a GA Rich 8x8 Nucleotide RNA Internal Loop
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 | 3.1 mM None RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3') | 95% H2O/5% D2O | 0.1 M | 6.2 | ambient | 273 | Varian INOVA 600 |
2 | 2D 1H-1H TOCSY | 3.1 mM None RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3') | 95% H2O/5% D2O | 0.1 M | 6.2 | ambient | 273 | Varian INOVA 600 |
3 | 2D 1H-1H NOESY | 3.1 mM None RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3') | 100% D2O | 0.1 M | 6.2 | ambient | 283 | Varian INOVA 600 |
4 | 2D 1H-1H TOCSY | 3.1 mM None RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3') | 100% D2O | 0.1 M | 6.2 | ambient | 283 | Varian INOVA 600 |
5 | 2D 31P-1H COSY | 3.1 mM None RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3') | 100% D2O | 0.1 M | 6.2 | ambient | 283 | Varian INOVA 600 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 600 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest restraint energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 33 |
Representative Model | 1 (lowest restraint energy) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | collection | VNMR | 6.1C | Varian |
2 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
3 | processing | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
4 | chemical shift assignment | Sparky | Goddard | |
5 | data analysis | Sparky | Goddard | |
6 | refinement | Amber | 14 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |
7 | data analysis | Amber | 14 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |
8 | structure calculation | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |