6K84 | pdb_00006k84

Structure of anti-prion RNA aptamer

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	1.0 mM RNA (25-MER), 10 mM potassium phosphate, 10 mM potassium chloride, 10 uM DSS	95% H2O/5% D2O	10 mM	6.2	1 atm	278	Bruker AVANCE III 950
2	2D JR-HMBC	1.0 mM RNA (25-MER), 10 mM potassium phosphate, 10 mM potassium chloride, 10 uM DSS	95% H2O/5% D2O	10 mM	6.2	1 atm	288	Bruker AVANCE III 600
3	2D 1H-1H NOESY	1.0 mM RNA (25-MER), 10 mM potassium phosphate, 10 mM potassium chloride, 10 uM DSS	100% D2O	10 mM	6.2	1 atm	288	Bruker AVANCE III 600
4	2D DQF-COSY	1.0 mM RNA (25-MER), 10 mM potassium phosphate, 10 mM potassium chloride, 10 uM DSS	100% D2O	10 mM	6.2	1 atm	288	Bruker AVANCE III 600
5	2D 1H-1H TOCSY	1.0 mM RNA (25-MER), 10 mM potassium phosphate, 10 mM potassium chloride, 10 uM DSS	100% D2O	10 mM	6.2	1 atm	288	Bruker AVANCE III 600
6	2D 1H-13C HSQC	1.0 mM RNA (25-MER), 10 mM potassium phosphate, 10 mM potassium chloride, 10 uM DSS	100% D2O	10 mM	6.2	1 atm	288	Bruker AVANCE III 600

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III	600
2	Bruker	AVANCE III	950

NMR Refinement
Method	Details	Software
molecular dynamics		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	refinement	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
2	structure calculation	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
3	chemical shift assignment	Sparky		Goddard
4	peak picking	Sparky		Goddard