2MGN | pdb_00002mgn

Solution structure of a G-quadruplex bound to the bisquinolinium compound Phen-DC3

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	0.2-2.0 mM DNA, 0.2-2.0 mM PQ3	90% H2O/10% D2O	45	7		298
2	2D 1H-1H NOESY	0.2-2.0 mM DNA, 0.2-2.0 mM PQ3	100% D2O	45	7		298
3	2D 1H-1H TOCSY	0.2-2.0 mM DNA, 0.2-2.0 mM PQ3	100% D2O	45	7		298
4	2D 1H-13C HSQC	1.0 mM DNA, 1.0 mM [U-100% 13C]-CH3 PQ3	100% D2O	90	7		298
5	2D 13C-filtered HSQC-NOESY	1.0 mM DNA, 1.0 mM [U-100% 13C]-CH3 PQ3	100% D2O	90	7		298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AMX	600
2	Bruker	AMX	700

NMR Refinement
Method	Details	Software
DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics	Extracted distances from structure of free DNA (PDB entry 2A5P) were used during calculation	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	geometry optimization	Amber		Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
2	refinement	Amber		Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
3	structure solution	Amber		Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
4	chemical shift assignment	Sparky		Goddard
5	data analysis	Sparky		Goddard
6	peak picking	Sparky		Goddard
7	collection	TopSpin		Bruker Biospin
8	processing	TopSpin		Bruker Biospin
9	geometry optimization	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
10	refinement	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
11	structure solution	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore