2K8Z
Dimeric solution structure of the DNA loop d(TCGTTGCT)
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 | 0.1-2.0 mM DNA (5'-D(*DTP*DCP*DGP*DTP*DTP*DGP*DCP*DT)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 10 mM magnesium chloride | 90% H2O/10% D2O | 7 | ambient | 278 | ||
2 | 2D 1H-1H TOCSY | 0.1-2.0 mM DNA (5'-D(*DTP*DCP*DGP*DTP*DTP*DGP*DCP*DT)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 10 mM magnesium chloride | 90% H2O/10% D2O | 7 | ambient | 278 | ||
3 | 2D DQF-COSY | 0.1-2.0 mM DNA (5'-D(*DTP*DCP*DGP*DTP*DTP*DGP*DCP*DT)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 10 mM magnesium chloride | 90% H2O/10% D2O | 7 | ambient | 278 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DMX | 600 |
2 | Bruker | DPX | 800 |
NMR Refinement | ||
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Method | Details | Software |
molecular dynamics | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | all calculated structures submitted |
Conformers Calculated Total Number | 10 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | structure solution | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm | |
2 | structure solution | DYANA | Guntert, Braun and Wuthrich | |
3 | chemical shift assignment | Sparky | Goddard | |
4 | peak picking | Sparky | Goddard | |
5 | data analysis | Sparky | Goddard | |
6 | refinement | DYANA | Guntert, Braun and Wuthrich |