6XAH
Structure of a Stable Interstrand DNA Crosslink Involving an dA Amino Group and an Abasic Site
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 | 500 uM deoxyribonucleic acid | 100% D2O | 120 mM | 8 | 1 atm | 298 | Bruker AVANCE III 900 |
2 | 2D 1H-1H TOCSY | 500 uM deoxyribonucleic acid | 95% H2O/5% D2O | 120 mM | 8 | 1 atm | 298 | Bruker AVANCE III 900 |
3 | 2D 1H-1H NOESY | 500 uM deoxyribonucleic acid | 95% H2O/5% D2O | 120 mM | 8 | 1 atm | 278 | Bruker AVANCE III 900 |
4 | 2D 1H-1H COSY | 500 uM deoxyribonucleic acid | 100% D2O | 120 mM | 8 | 1 atm | 298 | Bruker AVANCE III 900 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE III | 900 |
NMR Refinement | ||
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Method | Details | Software |
molecular dynamics | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the least restraint violations |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman | |
2 | chemical shift assignment | Sparky | Goddard | |
3 | data analysis | Sparky | Goddard | |
4 | processing | TopSpin | Bruker Biospin | |
5 | data analysis | TopSpin | Bruker Biospin | |
6 | structure calculation | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman | |
7 | peak picking | Sparky | Goddard |