9GDM | pdb_00009gdm

Solution structure of a silver ion mediated DNA duplex with universal 7-deazapurine substitutions

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	0.8 mM DNA, 100 mM NaClO4, 100 mM TRIS, 14.5 mM AgNO3	90% H2O/10% D2O	100 mM	8.6	1 bar	298	Varian VNMRS 800
2	2D NOESY	0.8 mM DNA, 100 mM NaClO4, 100 mM TRIS, 14.5 mM AgNO3	100% D2O	100 mM	8.6	1 bar	298	Bruker AVANCE NEO 600
3	2D 1H-1H COSY	0.8 mM DNA, 100 mM NaClO4, 100 mM TRIS, 14.5 mM AgNO3	100% D2O	100 mM	8.6	1 bar	298	Bruker AVANCE NEO 600
4	2D 1H-1H TOCSY	0.8 mM DNA, 100 mM NaClO4, 100 mM TRIS, 14.5 mM AgNO3	100% D2O	100 mM	8.6	1 bar	298	Bruker AVANCE NEO 600
5	2D 1H-31P HPCOSY	0.8 mM DNA, 100 mM NaClO4, 100 mM TRIS, 14.5 mM AgNO3	100% D2O	100 mM	8.6	1 bar	298	Bruker AVANCE NEO 600

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE NEO	600
2	Varian	VNMRS	800

NMR Refinement
Method	Details	Software
simulated annealing		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 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	VnmrJ	4.2	Agilent
5	collection	TopSpin	4.1	Bruker
6	processing	TopSpin	4.1	Bruker
2	structure calculation	Amber	20	Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
3	chemical shift assignment	NMRFAM-SPARKY		Lee W, Tonelli M, Markley JL (National Magnetic Resonance Facility at Madison)
4	peak picking	NMRFAM-SPARKY		Lee W, Tonelli M, Markley JL (National Magnetic Resonance Facility at Madison)