6ASF | pdb_00006asf

NMR and Restrained Molecular Dynamics Determination of the Structure of an Aza-Benzimidazole Derivative Complex with the DNA Minor Groove of an -AAGATA- Sequence

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H NOESY 100MS	0.54 mM DNA hairpin, 10 mM Tris-d11 buffer, 10 mM sodium chloride, 0.14 mM EDTA, 0.4 mM DSS	100% D2O	0.5 mM	6.3	AMBIENT	285	Bruker AVANCE 600
2	2D 1H-1H NOESY 100MS	0.54 mM DNA hairpin, 10 mM Tris-d11 buffer, 10 mM sodium chloride, 0.14 mM EDTA, 0.4 mM DSS	100% D2O	0.5 mM	6.3	AMBIENT	285	Bruker AVANCE III 850
3	2D 1H-1H NOESY 50MS	0.54 mM DNA hairpin, 10 mM Tris-d11 buffer, 10 mM sodium chloride, 0.14 mM EDTA, 0.4 mM DSS	100% D2O	0.5 mM	6.3	AMBIENT	285	Bruker AVANCE 600
4	2D 1H-1H NOESY 50MS	0.54 mM DNA hairpin, 10 mM Tris-d11 buffer, 10 mM sodium chloride, 0.14 mM EDTA, 0.4 mM DSS	100% D2O	0.5 mM	6.3	AMBIENT	285	Bruker AVANCE III 850
5	2D 1H-1H NOESY 150MS	0.54 mM DNA hairpin, 10 mM Tris-d11 buffer, 10 mM sodium chloride, 0.14 mM EDTA, 0.4 mM DSS	100% D2O	0.5 mM	6.3	AMBIENT	285	Bruker AVANCE 600
6	2D 1H-1H NOESY 300MS	0.54 mM DNA hairpin, 10 mM Tris-d11 buffer, 10 mM sodium chloride, 0.14 mM EDTA, 0.4 mM DSS	100% D2O	0.5 mM	6.3	AMBIENT	285	Bruker AVANCE 600
7	2D 1H-1H CONSTANT TIME NOESY	0.54 mM DNA hairpin, 10 mM Tris-d11 buffer, 10 mM sodium chloride, 0.14 mM EDTA, 0.4 mM DSS	100% D2O	0.5 mM	6.3	AMBIENT	285	Bruker AVANCE 600
8	1D 31P	0.54 mM DNA hairpin, 10 mM Tris-d11 buffer, 10 mM sodium chloride, 0.14 mM EDTA, 0.4 mM DSS	100% D2O	0.5 mM	6.3	AMBIENT	285	Bruker AVANCE 600
9	1H, 31P-correlated 2D spectra (HPCOR)	0.54 mM DNA hairpin, 10 mM Tris-d11 buffer, 10 mM sodium chloride, 0.14 mM EDTA, 0.4 mM DSS	100% D2O	0.5 mM	6.3	AMBIENT	285	Bruker AVANCE 600
10	2D 1H-1H TOCSY	0.54 mM DNA hairpin, 10 mM Tris-d11 buffer, 10 mM sodium chloride, 0.14 mM EDTA, 0.4 mM DSS	100% D2O	0.5 mM	6.3	AMBIENT	285	Bruker AVANCE 600

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	600
2	Bruker	AVANCE III	850

NMR Refinement
Method	Details	Software
molecular dynamics		Amber

NMR Ensemble Information
Conformer Selection Criteria	all calculated structures submitted
Conformers Calculated Total Number	11
Conformers Submitted Total Number	11
Representative Model	1 (minimized average structure)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	chemical shift assignment	Sparky		Goddard,T.D.; Kneller,D.G.
2	structure calculation	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
3	chemical shift assignment	Sparky		Goddard,T.D.; Kneller,D.G.
4	peak picking	Sparky		Goddard,T.D.; Kneller,D.G.

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 R01GM157729.