6ED9
NMR structure for Sp1 transcription factor duplex 5'-d(TGGGCGGGA)
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D DQF-COSY | 650 uM DNA, 25 mM sodium chloride, 5 mM Na Phosphate, 0.5 mM EDTA | 100% D2O | 30 mM Na+ mM | 7.0 | 1 atm | 298 | Bruker AVANCE 800 |
2 | 2D 1H-1H TOCSY | 650 uM DNA, 25 mM sodium chloride, 5 mM Na Phosphate, 0.5 mM EDTA | 100% D2O | 30 mM Na+ mM | 7.0 | 1 atm | 298 | Bruker AVANCE 800 |
3 | 2D 1H-13C HSQC | 650 uM DNA, 25 mM sodium chloride, 5 mM Na Phosphate, 0.5 mM EDTA | 100% D2O | 30 mM Na+ mM | 7.0 | 1 atm | 298 | Bruker AVANCE 800 |
4 | 2D 1H-1H NOESY | 650 uM DNA, 25 mM sodium chloride, 5 mM Na Phosphate, 0.5 mM EDTA | 100% D2O | 30 mM Na+ mM | 7.0 | 1 atm | 298 | Bruker AVANCE 800 |
5 | 2D 1H-1H NOESY | 675 uM DNA, 25 mM sodium chloride, 5 mM Na Phosphate, 0.5 mM EDTA | 90% H2O/10% D2O | 30 mM Na+ mM | 7.0 | 1 atm | 298 | Bruker AVANCE III 850 |
6 | 2D ECOSY | 650 uM DNA, 25 mM sodium chloride, 5 mM Na Phosphate, 0.5 mM EDTA | 100% D2O | 30 mM Na+ mM | 7.0 | 1 atm | 298 | Bruker AVANCE III 850 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 800 |
2 | Bruker | AVANCE III | 850 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 20 |
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 | structure calculation | CYANA | 3.97 | Guntert, Mumenthaler and Wuthrich |
2 | refinement | Amber | 14.0 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman |
3 | chemical shift assignment | Sparky | Goddard | |
4 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
5 | data analysis | 3DNA | Lu | |
6 | collection | TopSpin | Bruker Biospin |