2O4Y | pdb_00002o4y

Solution structure of a DNA duplex containing the universal base 5-nitroindole-3-carboxamide

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	1.9 mM DNA, 20 mM phosphate buffer, 100 mM NaCl, 0.2 mM EDTA	100% D2O	100 mM NaCl, 20mM sodium phosphate	6.9	ambient	311
2	2D DQF-COSY	1.9 mM DNA, 20 mM phosphate buffer, 100 mM NaCl, 0.2 mM EDTA	100% D2O	100 mM NaCl, 20mM sodium phosphate	6.9	ambient	311
3	2D TOCSY	1.9 mM DNA, 20 mM phosphate buffer, 100 mM NaCl, 0.2 mM EDTA	100% D2O	100 mM NaCl, 20mM sodium phosphate	6.9	ambient	311
4	2D 1H-31P HETCOR	1.9 mM DNA, 20 mM phosphate buffer, 100 mM NaCl, 0.2 mM EDTA	100% D2O	100 mM NaCl, 20mM sodium phosphate	6.9	ambient	311
5	2D ROESY	1.9 mM DNA, 20 mM phosphate buffer, 100 mM NaCl, 0.2 mM EDTA	90% H2O/10% D2O	100 mM NaCl, 20mM sodium phosphate	6.9	ambient	287

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	600

NMR Refinement
Method	Details	Software
simulated annealing	The structures were determined using simulated annealing using molecular dynamics with 440 NOE distance restraints (144 intra-residue and 296 inter-residue), 16 hydrogen bonding distance restraints and 167 dihedral restraints.	Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with the least restraint violations,structures with the lowest energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	28
Representative Model	1 (lowest energy)

Additional NMR Experimental Information
Details	Model 1 is the best representative conformer based on lowest total energy. Model 2 is the best representative conformer based on restraint energy. Models 1 and 2 represent two different stacking configurations of the nitroindole base.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin	1.3	Bruker biospin corporation
2	processing	NMRPipe	2004	F. Delaglio, S. Grzesiek, G. Zhu, G.W. Vuister, J. Pfeifer and A. Bax
3	data analysis	Sparky	3.110	T.D. Goddard and D.G. Kneller
4	refinement	Amber	8.0	D.A. Case et al.

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.