2KRV
Solution structure of the E. coli tRNA-Arg1 (ICG) ASL containing the 2-thiocytidine modification
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 0.8 mM RNA (5'-R(*CP*UP*CP*GP*GP*(N)P*UP*IP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')-1 | 90% H2O/10% D2O | 20 | 6.8 | ambient | 298 | |
| 2 | 2D 1H-1H NOESY | 0.8 mM RNA (5'-R(*CP*UP*CP*GP*GP*(N)P*UP*IP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')-2 | 100% D2O | 20 | 6.8 | ambient | 298 | |
| 3 | 2D DQF-COSY | 0.8 mM RNA (5'-R(*CP*UP*CP*GP*GP*(N)P*UP*IP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')-2 | 100% D2O | 20 | 6.8 | ambient | 298 | |
| 4 | 2D 1H-1H COSY | 0.8 mM RNA (5'-R(*CP*UP*CP*GP*GP*(N)P*UP*IP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')-1 | 90% H2O/10% D2O | 20 | 6.8 | ambient | 298 | |
| 5 | 2D 1H-1H TOCSY | 0.8 mM RNA (5'-R(*CP*UP*CP*GP*GP*(N)P*UP*IP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')-1 | 90% H2O/10% D2O | 20 | 6.8 | ambient | 298 | |
| 6 | 2D 1H-13C HSQC | 0.8 mM RNA (5'-R(*CP*UP*CP*GP*GP*(N)P*UP*IP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')-2 | 100% D2O | 20 | 6.8 | ambient | 298 | |
| 7 | 2D 1H-31P HETCOR | 0.8 mM RNA (5'-R(*CP*UP*CP*GP*GP*(N)P*UP*IP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')-2 | 100% D2O | 20 | 6.8 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 600 |
| 2 | Bruker | AVANCE | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | XwinNMR | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (closest to the average) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | XwinNMR | Bruker Biospin | |
| 2 | collection | TopSpin | Bruker Biospin | |
| 3 | collection | VnmrJ | Varian | |
| 4 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 5 | processing | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 6 | chemical shift assignment | Sparky | Goddard | |
| 7 | data analysis | Sparky | Goddard | |
| 8 | peak picking | Sparky | Goddard | |
| 9 | structure solution | CNS | 1.21 | Brunger, Adams, Clore, Gros, Nilges and Read |
| 10 | data analysis | MOLMOL | Koradi, Billeter and Wuthrich | |
| 11 | refinement | CNS | 1.21 | Brunger, Adams, Clore, Gros, Nilges and Read |
