Experiment: 7LVA

Solution structure of the HIV-1 PBS-segment

SOLUTION NMR - SOLUTION SCATTERING

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H NOESY	250 uM 1H RNA (103-MER)	100% D2O	3 mM	7.5	1 atm	308	Bruker AVANCE 800
2	2D 1H-1H NOESY	250 uM A-8D, C-D, G-H, U-5,6-D2 RNA (103-MER)	100% D2O	3 mM	7.5	1 atm	308	Bruker AVANCE 800
3	2D 1H-1H NOESY	250 uM A-8D, C-D, G-8D, U-H RNA (103-MER)	100% D2O	3 mM	7.5	1 atm	308	Bruker AVANCE 800
4	2D 1H-1H NOESY	250 uM A-8D, C-5,6-D2, G-D, U-5,6-D2 RNA (103-MER)	100% D2O	3 mM	7.5	1 atm	308	Bruker AVANCE 800
5	2D 1H-1H NOESY	250 uM A-8D, C-D, G-8D, U-D RNA (103-MER)	100% D2O	3 mM	7.5	1 atm	308	Bruker AVANCE 800
6	2D 1H-1H NOESY	250 uM A-H, C-D, G-H, U-D RNA (103-MER)	100% D2O	3 mM	7.5	1 atm	308	Bruker AVANCE 800
7	2D 1H-1H NOESY	250 uM A-H, C-H, G-D, U-D RNA (103-MER)	100% D2O	3 mM	7.5	1 atm	308	Bruker AVANCE 800

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	800

NMR Refinement
Method	Details	Software
molecular dynamics	Structure minimization	Amber
distance geometry	The SAXS scattering profiles for each structure were back calculated and the structures with lowest chi2 compared with experimental SAXS data were selected.	X-PLOR NIH

NMR Ensemble Information
Conformer Selection Criteria	target function
Conformers Calculated Total Number	1200
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
5	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
6	processing	NMRDraw		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
7	chemical shift assignment	NMRView		Johnson, One Moon Scientific
8	peak picking	NMRView		Johnson, One Moon Scientific
1	structure calculation	CYANA		Guntert, Mumenthaler and Wuthrich
9	geometry optimization	CYANA		Guntert, Mumenthaler and Wuthrich
4	refinement	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman
2	refinement	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore