8Y0F
Solution NMR structure of the PTK7-binding DNA aptamer sgc8c
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 | 0.5 mM DNA, 0.02 mM DSS, 10 mM sodium phosphate, 5 mM Magnesium chloride | 99.96%D2O | 15 mM | 7 | 1 bar | 277 | Bruker AVANCE 600 |
2 | 2D 1H-1H COSY | 0.5 mM DNA, 0.02 mM DSS, 10 mM sodium phosphate, 5 mM Magnesium chloride | 99.96%D2O | 15 mM | 7 | 1 bar | 277 | Bruker AVANCE 600 |
3 | 2D 1H-1H TOCSY | 0.5 mM DNA, 0.02 mM DSS, 10 mM sodium phosphate, 5 mM Magnesium chloride | 99.96%D2O | 15 mM | 7 | 1 bar | 277 | Bruker AVANCE 600 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | GROMACS | |
restrained energy minimization | Amber |
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 (closest to the average) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | chemical shift assignment | TopSpin | Bruker Biospin | |
2 | structure calculation | GROMACS | Abraham, Alekseenko, Bauer, Bergh, Blau, Briand, Doijade,... and Zhmurov | |
3 | refinement | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |