8Y0F | pdb_00008y0f

Solution NMR structure of the PTK7-binding DNA aptamer sgc8c

SOLUTION NMR

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NMR Experiment
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
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	600

NMR Refinement
Method	Details	Software
simulated annealing		GROMACS
restrained energy minimization		Amber

NMR Ensemble Information
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
#	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