7N7D | pdb_00007n7d

Solution structure of the MYC promoter G-quadruplex in complex with berberine: conformer A

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	1.2 mM DNA, 3.6 mM Berberine, 10 mM potassium phosphate	90% H2O/10% D2O	10 mM	7	1 atm	298	Bruker AVANCE III 800
2	2D 1H-1H NOESY	1.2 mM DNA, 3.6 mM Berberine, 10 mM potassium phosphate	90% H2O/10% D2O	10 mM	7	1 atm	308	Bruker AVANCE III 800
3	2D 1H-13C HSQC aromatic	1.2 mM DNA, 3.6 mM Berberine, 10 mM potassium phosphate	90% H2O/10% D2O	10 mM	7	1 atm	298	Bruker AVANCE III 800

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III	800

NMR Refinement
Method	Details	Software
simulated annealing		X-PLOR NIH
simulated annealing		Amber
molecular dynamics		Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	20
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	Amber	16	Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman
6	structure calculation	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman
2	structure calculation	X-PLOR NIH	2.48	Schwieters, Kuszewski, Tjandra and Clore
3	chemical shift assignment	CcpNmr Analysis	2.4	CCPN
4	peak picking	CcpNmr Analysis	2.4	CCPN
5	processing	TopSpin		Bruker Biospin