Experiment: 2JTP

Solution Structure of the Frameshift-Inducing RNA Stem-Loop in SIV

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H TOCSY	1 mM SIV17-50 RNA (34-MER)	100% D2O		7.0	ambient	308
2	2D 1H-1H NOESY	1 mM SIV17-50 RNA (34-MER)	100% D2O		7.0	ambient	308
3	2D 1H-1H COSY	1 mM SIV17-50 RNA (34-MER)	90% H2O/10% D2O		7.0	ambient	308
4	2D 1H-15N HSQC	1 mM [U-100% 13C; U-100% 15N] SIV17-50 RNA (34-MER)	100% D2O		7.0	ambient	308
5	2D 1H-13C HSQC	1 mM [U-100% 13C; U-100% 15N] SIV17-50 RNA (34-MER)	100% D2O		7.0	ambient	308
6	3D 1H-13C-1H HCCH-TOCSY	1 mM [U-100% 13C; U-100% 15N] SIV17-50 RNA (34-MER)	100% D2O		7.0	ambient	308
7	3D NOESY-HMQC	1 mM [U-100% 13C; U-100% 15N] SIV17-50 RNA (34-MER)	100% D2O		7.0	ambient	308
8	J-MODULATED 1H-13C CT-HSQC	1 mM [U-100% 13C; U-100% 15N] SIV17-50 RNA (34-MER)	90% H2O/10% D2O		7.0	ambient	308
9	J-MODULATED 1H-13C CT-HSQC	1 mM [U-100% 13C; U-100% 15N] SIV17-50 RNA (34-MER)	90% H2O/10% D2O		7.0	ambient	308
10	2D 1H-1H NOESY	1 mM SIV17-50 RNA (34-MER)	90% H2O/10% D2O		7.0	ambient	308

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	DMX	750
2	Bruker	DMX	600
3	Varian	INOVA	600
4	Varian	INOVA	800
5	Bruker	DMX	500
6	Varian	INOVA	900

NMR Refinement
Method	Details	Software
simulated annealing, torsion angle dynamics, molecular dynamics, residual dipolar couplings		XwinNMR

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	20
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	XwinNMR	3.5	Bruker Biospin
2	processing	XwinNMR	3.5	Bruker Biospin
3	peak picking	Sparky	3.111	Goddard
4	data analysis	Sparky	3.111	Goddard
5	structure solution	CNS	1.1	Brunger, Adams, Clore, Gros, Nilges and Read
6	refinement	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
7	structure solution	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
8	collection	VNMR		Varian
9	processing	NMRDraw		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
10	peak picking	NMRDraw		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
11	data analysis	NMRDraw		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax