9P9X | pdb_00009p9x

Solution structure of the major PDGFRB promoter G-quadruplex with a broken-strand G22 fill-in

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	75 mM potassium chloride, 25 mM potassium phosphate, 0.73 mM DNA (5'-D(*AP*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*GP*CP*AP*GP*GP*G)-3')	90% H2O/10% D2O	100 mM	7.0	1 atm	298	Bruker AVANCE III 800
2	2D 1H-1H NOESY	75 mM potassium chloride, 25 mM potassium phosphate, 0.73 mM DNA (5'-D(*AP*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*GP*CP*AP*GP*GP*G)-3')	90% H2O/10% D2O	100 mM	7.0	1 atm	313	Bruker AVANCE III 800
3	2D 1H-13C HSQC	75 mM potassium chloride, 25 mM potassium phosphate, 0.73 mM DNA (5'-D(*AP*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*GP*CP*AP*GP*GP*G)-3')	90% H2O/10% D2O	100 mM	7.0	1 atm	313	Bruker AVANCE III 800
4	2D 1H-1H NOESY	10 mM potassium phosphate, 1.63 mM DNA (5'-D(*AP*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*GP*CP*AP*GP*GP*G)-3')	90% H2O/10% D2O	10 mM	7.0	1 atm	298	Bruker AVANCE III 800
5	2D 1H-13C HSQC	10 mM potassium phosphate, 1.63 mM DNA (5'-D(*AP*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*GP*CP*AP*GP*GP*G)-3')	90% H2O/10% D2O	10 mM	7.0	1 atm	298	Bruker AVANCE III 800
6	2D 1H-1H NOESY	75 mM potassium chloride, 25 mM potassium phosphate, 1.36 mM DNA (5'-D(*AP*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*GP*CP*AP*GP*GP*G)-3')	90% H2O/10% D2O	100 mM	7.0	1 atm	283	Bruker AVANCE III 800

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

NMR Refinement
Method	Details	Software
simulated annealing		Amber
simulated annealing		X-PLOR NIH
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	chemical shift assignment	CcpNmr Analysis	2.4	CCPN
2	peak picking	CcpNmr Analysis	2.4	CCPN
3	processing	TopSpin		Bruker Biospin
4	structure calculation	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman
5	refinement	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman
6	structure calculation	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore