2M23 | pdb_00002m23

NMR solution structure of the d3'-hairpin of the group II intron Sc.ai5gamma including EBS1 bound to IBS1

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	0.5-0.9 mM RNA (29-MER), 0.5-0.9 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	100% D2O	110	6.8	ambient	298
2	2D 1H-1H NOESY	0.5-0.9 mM RNA (29-MER), 0.5-0.9 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	100% D2O	110	6.8	ambient	298
3	2D 1H-1H TOCSY	0.5-0.9 mM RNA (29-MER), 0.5-0.9 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	100% D2O	110	6.8	ambient	298
4	2D 1H-1H NOESY	0.6 mM [3',4',5',5'',5-100% 2H] RNA (29-MER), 0.6 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	100% D2O	110	6.8	ambient	298
5	2D 1H-13C HSQC aliphatic	0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	110	6.8	ambient	298
6	2D 1H-13C HSQC aliphatic	0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 25.6 mg/mL Pf1 phage	90% H2O/10% D2O	110	6.8	ambient	298
7	2D 1H-15N HSQC	0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	110	6.8	ambient	278
8	2D 1H-13C HSQC aromatic	0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	110	6.8	ambient	298
9	2D 1H-13C HSQC aromatic	0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 25.6 mg/mL Pf1 phage	90% H2O/10% D2O	110	6.8	ambient	298
10	2D 1H-13C HSQC aliphatic	0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	100% D2O	110	6.8	ambient	298
11	2D 1H-13C HSQC aromatic	0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	100% D2O	110	6.8	ambient	298
12	2D 1H-1H NOESY	0.5-0.9 mM RNA (29-MER), 0.5-0.9 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	110	6.8	ambient	278
13	2D 1H-1H NOESY	0.5-0.9 mM RNA (29-MER), 0.5-0.9 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	110	6.8	ambient	278
14	2D 1H-1H NOESY	0.5-0.9 mM RNA (29-MER), 0.5-0.9 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	110	6.8	ambient	293
15	2D JNN HNN COSY	0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	110	6.8	ambient	278
16	1D-31P	0.5-0.9 mM RNA (29-MER), 0.5-0.9 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	100% D2O	110	6.8	ambient	298
17	F1,2 X-filtered 1H-1H NOESY	0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	110	6.8	ambient	298
18	F1,2 X-filtered 1H-1H TOCSY	0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA	90% H2O/10% D2O	110	6.8	ambient	298

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		Sparky

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