2M24

NMR solution structure of the d3'-hairpin including the exon binding site 1 (EBS1) of the group II intron Sc.ai5gamma

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H NOESY	0.4-1.2 mM RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA	100% D2O	10	6.8	ambient	293
2	2D 1H-1H TOCSY	0.4-1.2 mM RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA	100% D2O	10	6.8	ambient	293
3	2D 1H-1H NOESY	0.4-1.2 mM RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA	100% D2O	10	6.8	ambient	293
4	2D 1H-1H NOESY	0.4-1.2 mM RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	10	6.8	ambient	278
5	2D 1H-1H NOESY	0.4-1.2 mM RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	10	6.8	ambient	278
6	2D 1H-13C HSQC aliphatic	0.7 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	10	6.8	ambient	298
7	2D 1H-13C HSQC aromatic	0.7 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	10	6.8	ambient	298
8	2D 1H-15N HSQC	0.7 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	10	6.8	ambient	278
9	2D 1H-13C HSQC aliphatic	0.7 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 25.6 mg/mL Pf1 phage	90% H2O/10% D2O	10	6.8	ambient	298
10	2D 1H-13C HSQC aromatic	0.7 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 25.6 mg/mL Pf1 phage	90% H2O/10% D2O	10	6.8	ambient	298
11	2D JNN HNN COSY	0.7 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	10	6.8	ambient	278
12	2D 1H-1H NOESY	0.4-1.2 mM RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA	100% D2O	10	6.8	ambient	283
13	2D 1H-1H NOESY	0.4-1.2 mM RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA	100% D2O	10	6.8	ambient	298
14	1D 31P	0.4-1.2 mM RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA	100% D2O	10	6.8	ambient	293
15	2D 1H-1H NOESY	0.6 mM [3',4',5',5'',5, 100% 2H] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA	100% D2O	10	6.8	ambient	293
16	2D 1H-13C HSQC	0.7 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA	100% D2O	10	6.8	ambient	293

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	700
2	Bruker	AVANCE	600
3	Bruker	AVANCE	500

NMR Refinement
Method	Details	Software
molecular dynamics, torsion angle dynamics		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	collection	TopSpin	1.3, 2.0, 2.1	Bruker Biospin
2	processing	TopSpin	1.3, 2.0, 2.1	Bruker Biospin
3	chemical shift assignment	Sparky	3.1	Goddard
4	data analysis	Sparky	3.1	Goddard
5	peak picking	Sparky	3.1	Goddard
6	data analysis	DYANA	1.5	Guntert, Braun and Wuthrich
7	structure solution	CNSSOLVE	1.2	Brunger, Adams, Clore, Gros, Nilges and Read
8	refinement	CNSSOLVE	1.2	Brunger, Adams, Clore, Gros, Nilges and Read
9	structure solution	X-PLOR NIH	2.24	Schwieters, Kuszewski, Tjandra and Clore
10	refinement	X-PLOR NIH	2.24	Schwieters, Kuszewski, Tjandra and Clore

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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.