2K65

NMR solution structure of the exon/intron binding site 1 (EBS1/IBS1) 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	0.8-0.9 mM RNA (7A-MER), 0.8-0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA	100% D2O	100	6.3	ambient	288
2	2D 1H-1H NOESY	0.8-0.9 mM RNA (7A-MER), 0.8-0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA	100% D2O	100	6.3	ambient	293
3	2D 1H-1H NOESY	0.8-0.9 mM RNA (7A-MER), 0.8-0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA	100% D2O	100	6.3	ambient	298
4	2D 1H-1H TOCSY	0.8-0.9 mM RNA (7A-MER), 0.8-0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA	100% D2O	100	6.3	ambient	288
5	2D 1H-1H TOCSY	0.8-0.9 mM RNA (7A-MER), 0.8-0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA	100% D2O	100	6.3	ambient	293
6	2D 1H-1H TOCSY	0.8-0.9 mM RNA (7A-MER), 0.8-0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA	100% D2O	100	6.3	ambient	298
7	2D 1H-1H NOESY	0.9 mM RNA (7A-MER), 0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	100	6.3	ambient	278
8	2D 1H-13C HSQC	0.8-0.9 mM RNA (7A-MER), 0.8-0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA	100% D2O	100	6.3	ambient	288

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.