5O4D | pdb_00005o4d

G-quadruplex of Human papillomavirus type 52

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 (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*CP*AP*GP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*T)-3'), 10 mM potassium phosphate, 40 mM potassium chloride	90% H2O/10% D2O	50 mM	6.8	1 atm	298	Varian VNMRS 800
2	2D 1H-1H NOESY	1.2 mM DNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*CP*AP*GP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*T)-3'), 10 mM potassium phosphate, 40 mM potassium chloride	100% D2O	50 mM	6.8	1 atm	298	Varian VNMRS 800
3	2D 1H-1H TOCSY	1.2 mM DNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*CP*AP*GP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*T)-3'), 10 mM potassium phosphate, 40 mM potassium chloride	100% D2O	50 mM	6.8	1 atm	298	Varian VNMRS 800
4	2D DQF-COSY	1.2 mM DNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*CP*AP*GP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*T)-3'), 10 mM potassium phosphate, 40 mM potassium chloride	100% D2O	50 mM	6.8	1 atm	298	Varian VNMRS 800
5	2D HP COSY	1.2 mM DNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*CP*AP*GP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*T)-3'), 10 mM potassium phosphate, 40 mM potassium chloride	100% D2O	50 mM	6.8	1 atm	298	Varian DD2 600
6	2D 1H-13C HSQC aromatic	0.9 mM 15N site-specifically labelled at 5% DNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*CP*AP*GP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*T)-3'), 10 mM potassium phosphate, 40 mM potassium chloride	100% D2O	50 mM	6.8	1 atm	298	Varian VNMRS 800

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	VNMRS	800
2	Varian	DD2	600

NMR Refinement
Method	Details	Software
simulated annealing		Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with lowest energy and least restraint violations
Conformers Calculated Total Number	1000
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	VnmrJ	3.	Agilent
2	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3	peak picking	Sparky	3.115	Goddard
4	data analysis	Sparky	3.115	Goddard
5	structure calculation	Amber	14	Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
6	refinement	Amber	14	Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
7	chemical shift assignment	Sparky	3.115	Goddard