2KRY
Solution structure of the human mitochondrial tRNAMet ASL containing the 5-formylcytidine modification in position 34
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 1.0 mM RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(RSQ)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3')-1 | 90% H2O/10% D2O | 20 | 6.8 | ambient | 298 | |
2 | 2D 1H-1H NOESY | 1 mM RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(RSQ)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3')-2 | 100% D2O | 20 | 6.8 | ambient | 298 | |
3 | 2D DQF-COSY | 1 mM RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(RSQ)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3')-2 | 100% D2O | 20 | 6.8 | ambient | 298 | |
4 | 2D 1H-1H COSY | 1.0 mM RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(RSQ)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3')-1 | 90% H2O/10% D2O | 20 | 6.8 | ambient | 298 | |
5 | 2D 1H-1H TOCSY | 1.0 mM RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(RSQ)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3')-1 | 90% H2O/10% D2O | 20 | 6.8 | ambient | 298 | |
6 | 2D 1H-13C HSQC | 1 mM RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(RSQ)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3')-2 | 100% D2O | 20 | 6.8 | ambient | 298 | |
7 | 2D 1H-31P HETCOR | 1 mM RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(RSQ)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-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 (lowest energy) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | collection | XwinNMR | Bruker Biospin | |
2 | collection | TopSpin | Bruker Biospin | |
3 | data analysis | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
4 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
5 | peak picking | Sparky | Goddard | |
6 | chemical shift assignment | Sparky | Goddard | |
7 | data analysis | Sparky | Goddard | |
8 | structure solution | CNS | 1.21 | Brunger, Adams, Clore, Gros, Nilges and Read |
9 | data analysis | MOLMOL | Koradi, Billeter and Wuthrich | |
10 | refinement | CNS | 1.21 | Brunger, Adams, Clore, Gros, Nilges and Read |