2K5Z

Solution structure and dynamics of the apical stem-loop of Duck hepatitis B virus

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H NOESY	1.2 mM Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 95% H2O, 5% D2O	95% H2O/5% D2O	10	6.7	ambient	278
2	2D 1H-1H NOESY	1.2 mM Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 100% D2O	100% D2O	10	6.7	ambient	298
3	3D 1H-13C NOESY	0.7 mM [U-13C; U-15N] Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 5% D2O, 95% H2O, 1 mM DSS	95% H2O/5% D2O	10	6.7	ambient	288
4	2D 1H-15N HSQC	1 mM [U-13C; U-15N]-Ura Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 5% D2O, 95% H2O	95% H2O/5% D2O	10	6.7	ambient	278
5	2D 1H-15N HSQC	0.7 mM [U-13C; U-15N] Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 5% D2O, 95% H2O, 1 mM DSS	95% H2O/5% D2O	10	6.7	ambient	288
6	2D 1H-13C HSQC	1.2 mM Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 100% D2O	100% D2O	10	6.7	ambient	298
7	2D 1H-13C HSQC	1 mM [U-13C; U-15N]-Ura Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 100% D2O	100% D2O	10	6.7	ambient	298
8	2D 1H-13C HSQC	0.7 mM [U-13C; U-15N] Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 5% D2O, 95% H2O, 1 mM DSS	95% H2O/5% D2O	10	6.7	ambient	288
9	2D DQF-COSY	1.2 mM Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 100% D2O	100% D2O	10	6.7	ambient	298
10	2D 1H-1H COSY	0.7 mM [U-13C; U-15N] Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 5% D2O, 95% H2O, 1 mM DSS	95% H2O/5% D2O	10	6.7	ambient	288
11	3D HCCH-TOCSY	0.7 mM [U-13C; U-15N] Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 5% D2O, 95% H2O, 1 mM DSS	95% H2O/5% D2O	10	6.7	ambient	288
12	3D HCN	0.7 mM [U-13C; U-15N] Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 5% D2O, 95% H2O, 1 mM DSS	95% H2O/5% D2O	10	6.7	ambient	288

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	500
2	Varian	INOVA	600
3	Varian	INOVA	800

NMR Refinement
Method	Details	Software
torsion angle dynamics	RDC refinement	Sparky

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	chemical shift assignment	Sparky		Goddard
2	peak picking	Sparky		Goddard
3	processing	NMRDraw		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
4	structure solution	X-PLOR	3.851	Brunger
5	refinement	X-PLOR	3.851	Brunger

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.