9U89 | pdb_00009u89

Structure of AA(GGGTT)3GGGAA G-quadruplex in the presence of potassium ions

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	1.5 mM DNA (5'-D(*AP*AP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*A)-3'), 20 mM potassium phosphate, 50 mM potassium chloride, 50 uM DSS	95% H2O/5% D2O	418 mM	7	1 atm	298	Bruker AVANCE III 700
2	2D 1H-13C HSQC	1.5 mM DNA (5'-D(*AP*AP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*A)-3'), 20 mM potassium phosphate, 50 mM potassium chloride, 50 uM DSS	95% H2O/5% D2O	418 mM	7	1 atm	298	Bruker AVANCE III 700
3	2D DQF-COSY	1.5 mM DNA (5'-D(*AP*AP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*A)-3'), 20 mM potassium phosphate, 50 mM potassium chloride, 50 uM DSS	95% H2O/5% D2O	418 mM	7	1 atm	298	Bruker AVANCE III 700
4	2D 1H-15N HMQC	1.5 mM DNA (5'-D(*AP*AP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*A)-3'), 20 mM potassium phosphate, 50 mM potassium chloride, 50 uM DSS	95% H2O/5% D2O	418 mM	7	1 atm	298	Bruker AVANCE III 700
5	2D 1H-13C HSQC F2 coupled	1.5 mM DNA (5'-D(*AP*AP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*A)-3'), 20 mM potassium phosphate, 50 mM potassium chloride, 50 uM DSS	95% H2O/5% D2O	418 mM	7	1 atm	298	Bruker AVANCE III 700
6	2D 1H-15N HMQC F2 coupled	1.5 mM DNA (5'-D(*AP*AP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*A)-3'), 20 mM potassium phosphate, 50 mM potassium chloride, 50 uM DSS	95% H2O/5% D2O	418 mM	7	1 atm	298	Bruker AVANCE III 700
7	2D 1H-13C HSQC F2 coupled	1.5 mM DNA (5'-D(*AP*AP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*A)-3'), 20 mM potassium phosphate, 50 mM potassium chloride, 50 uM DSS	95% H2O/5% D2O	418 mM	7	1 atm	298	Bruker AVANCE III 700
8	2D 1H-15N HMQC F2 coupled	1.5 mM DNA (5'-D(*AP*AP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*A)-3'), 20 mM potassium phosphate, 50 mM potassium chloride, 50 uM DSS	95% H2O/5% D2O	418 mM	7	1 atm	298	Bruker AVANCE III 700

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III	700

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

NMR Ensemble Information
Conformer Selection Criteria	structures with the least restraint violations
Conformers Calculated Total Number	50
Conformers Submitted Total Number	5
Representative Model	1 (fewest violations)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin	3.6	Bruker Biospin
2	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3	chemical shift assignment	NMRFAM-SPARKY		Lee W, Tonelli M, Markley JL
4	peak picking	NMRFAM-SPARKY		Lee W, Tonelli M, Markley JL
5	geometry optimization	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
6	structure calculation	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
7	refinement	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman