6MCF

Solution structure of 7SK stem-loop 1 with HIV-1 Tat RNA Binding Domain

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 mM 7SK Stem-loop 1 RNA, 0.5 mM HIV-1 Tat RNA Binding Domain	90% H2O/10% D2O	10mM phosphates, 70mM NaCl mM	5.4	100000 Pa	298	Bruker DMX 700
5	2D 1H-1H NOESY	0.5 mM 7SK Stem-loop 1 RNA, 0.5 mM HIV-1 Tat RNA Binding Domain	100% D2O	10mM phosphates, 70mM NaCl mM	5.4	100000 Pa	298	Bruker DMX 700
2	2D 1H-15N HSQC	0.5 mM 7SK Stem-loop 1 RNA, 0.5 mM [U-13C; U-15N] HIV-1 Tat RNA Binding Domain selectively labeled with the following schema: 1) R49, K50, R57, A58 2) K51, R52, Q54, R55 3) R53, Q54, R56	90% H2O/10% D2O	10mM phosphates, 70mM NaCl mM	5.4	100000 Pa	298	Bruker DMX 700
3	2D 1H-15N HSQC	0.5 mM [U-13C; U-15N] 7SK Stem-loop 1 RNA, 0.5 mM HIV-1 Tat RNA Binding Domain	90% H2O/10% D2O	10mM phosphates, 70mM NaCl mM	5.4	100000 Pa	298	Bruker DMX 700
4	2D 1H-13C HSQC	0.5 mM 7SK Stem-loop 1 RNA, 0.5 mM [U-13C; U-15N] HIV-1 Tat RNA Binding Domain selectively labeled with the following schema: 1) R49, K50, R57, A58 2) K51, R52, Q54, R55 3) R53, Q54, R56	100% D2O	10mM phosphates, 70mM NaCl mM	5.4	100000 Pa	298	Bruker DMX 700
6	2D 1H-13C HSQC	0.5 mM [U-13C; U-15N] 7SK Stem-loop 1 RNA, 0.5 mM HIV-1 Tat RNA Binding Domain	100% D2O	10mM phosphates, 70mM NaCl mM	5.4	100000 Pa	298	Bruker DMX 700

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

NMR Refinement
Method	Details	Software
simulated annealing		Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with the least restraint violations
Conformers Calculated Total Number	20
Conformers Submitted Total Number	10
Representative Model	1 (fewest violations)

Computation: NMR Software
#	Classification	Version	Software Name	Author
7	collection	TopSpin		Bruker Biospin
1	peak picking	NMRView		Johnson, One Moon Scientific
2	chemical shift assignment	NMRView		Johnson, One Moon Scientific
3	data analysis	CYANA		Guntert, Mumenthaler and Wuthrich
4	processing	CYANA		Guntert, Mumenthaler and Wuthrich
5	structure calculation	CYANA		Guntert, Mumenthaler and Wuthrich
6	refinement	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman