2KH6
Solution Structure of cis-5R,6S-thymine glycol opposite complementary adenine in duplex DNA
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 | 20 mM sodium phosphate-1, 100 mM sodium chloride-2, 10 uM sodium azide-3, 50 uM EDTA-4 | 100% D2O | 0.1 | 7.0 | ambient | 303 | |
2 | 2D 1H-1H COSY | 20 mM sodium phosphate-1, 100 mM sodium chloride-2, 10 uM sodium azide-3, 50 uM EDTA-4 | 100% D2O | 0.1 | 7.0 | ambient | 303 | |
3 | 2D 1H-1H NOESY | 20 mM sodium phosphate-5, 100 mM sodium chloride-6, 10 uM sodium azide-7, 50 uM EDTA-8 | 90% H2O/10% D2O | 0.1 | 7.0 | ambient | 278 | |
4 | 2D 31P-1H COSY | 20 mM sodium phosphate-1, 100 mM sodium chloride-2, 10 uM sodium azide-3, 50 uM EDTA-4 | 100% D2O | 0.1 | 7.0 | ambient | 303 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 800 |
2 | Bruker | AVANCE | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing, molecular dynamics | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | back calculated data agree with experimental NOESY spectrum |
Conformers Calculated Total Number | 10 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (closest to the average) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | Amber | 9 | Delaglio, Zhengrong and Bax |
2 | chemical shift assignment | Sparky | Goddard | |
3 | data analysis | Sparky | Goddard | |
4 | processing | TopSpin | Bruker Biospin | |
5 | restraint generation | MARDIGRAS | Borgias, B.A. & James, T.L. | |
6 | structure validation | CORMA | James T.L. | |
7 | data analysis | Curves | Lavery, R. and Sklenar, H | |
8 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |