2K66

NMR solution structure of the d3'-stem closed by a GAAA tetraloop of the group II intron Sc.ai5(gamma)

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H NOESY	0.9-1.3 mM RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA	100% D2O	10	6.0-6.1	ambient	293
2	2D 1H-1H NOESY	0.9-1.3 mM RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA	100% D2O	10	6.0-6.1	ambient	303
3	2D 1H-1H TOCSY	0.9-1.3 mM RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA	100% D2O	10	6.0-6.1	ambient	293
4	2D 1H-1H TOCSY	0.9-1.3 mM RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA	100% D2O	10	6.0-6.1	ambient	303
5	2D 1H-1H NOESY	0.9-1.3 mM RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	10	6.2	ambient	278
6	2D 1H-1H NOESY	0.9-1.3 mM RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	10	6.2	ambient	293
7	2D 1H-13C HSQC	1.0 mM [U-100% 13C; U-100% 15N] RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA	100% D2O	10	6.4	ambient	303
8	2D 1H-15N HSQC	1.0 mM [U-100% 13C; U-100% 15N] RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	10	6.4	ambient	278
9	2D JNN HNN-COSY	1.0 mM [U-100% 13C; U-100% 15N] RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	Avance	700

NMR Refinement
Method	Details	Software
torsion angle dynamics, simulated annealing		TOPSPIN

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	200
Conformers Submitted Total Number	20
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	TOPSPIN	1.3, 2.0, 2.1	Bruker Biospin
2	chemical shift assignment	SPARKY	3.1	Goddard
3	data analysis	SPARKY	3.1	Goddard
4	peak picking	SPARKY	3.1	Goddard
5	structure solution	DYANA	1.5	Guntert, Braun and Wuthrich
6	structure solution	CNSSOLVE	1.2	Brunger, Adams, Clore, Gros, Nilges and Read
7	refinement	X-PLOR_NIH	2.16	Schwieters, Kuszewski, Tjandra and Clore

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.