5YEY
The structure of a chair-type G-quadruplex of the human telomeric variant in K+ solution
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 | 2.5 mM DNA (5'-D(*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3') | 90% H2O/10% D2O | 90 mM | 7 | ambient Pa | 284 | Varian INOVA 800 |
2 | 2D 1H-1H NOESY | 2.5 mM DNA (5'-D(*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3') | 100% D2O | 90 mM | 7 | ambient Pa | 284 | Varian INOVA 800 |
3 | 2D 1H-1H TOCSY | 2.5 mM DNA (5'-D(*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3') | 100% D2O | 90 mM | 7 | ambient Pa | 284 | Varian INOVA 500 |
4 | 2D 1H-1H COSY | 2.5 mM DNA (5'-D(*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3') | 100% D2O | 90 mM | 7 | ambient Pa | 284 | Varian INOVA 800 |
5 | 2D 1H-13C HSQC | 2.5 mM DNA (5'-D(*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3') | 100% D2O | 90 mM | 7 | ambient Pa | 284 | Varian INOVA 800 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 800 |
2 | Varian | INOVA | 500 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing | the structures are based on a total of 304 distance constriants | X-PLOR NIH |
NMR Ensemble Information | |
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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 | VNMR | Varian | |
2 | chemical shift calculation | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
3 | chemical shift assignment | Sparky | Goddard | |
4 | peak picking | Sparky | Goddard | |
5 | data analysis | Sparky | Goddard | |
6 | structure calculation | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
7 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore |