Experiment: 2L8P

Solution Structure of a DNA Duplex Containing the Potent Anti-Poxvirus Agent Cidofovir

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H NOESY	2 mM Cidofovir DNA duplex	95% H2O/5% D2O	70	7.0-7.2	ambient	298
2	2D 1H-1H TOCSY	2 mM Cidofovir DNA duplex	95% H2O/5% D2O	70	7.0-7.2	ambient	298
3	2D DQF-COSY	2 mM Cidofovir DNA duplex	95% H2O/5% D2O	70	7.0-7.2	ambient	298
4	2D DQF-COSY	2 mM Cidofovir DNA duplex	95% H2O/5% D2O	70	7.0-7.2	ambient	298
5	2D 1H-13C HSQC	2 mM Cidofovir DNA duplex	95% H2O/5% D2O	70	7.0-7.2	ambient	298

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

NMR Refinement
Method	Details	Software
simulated annealing	The upper bounds obtained from MARDIGRAS were multiplied by a factor 1.25 before being exported to Amber 10 for a 25 ps simulated annealing protocol. The simulated annealing protocol using the pairwise generalized Born model was as follows: the temperature of the system was kept constant at 600 K during the first 5 ps, cooled down slowly to 100 K between 5-18 ps, and cooled down to 0 K for the last 7 ps. The protocol was repeated 50 times to obtain an NMR ensemble with the 10 lowest RMSD structures. The structure with the lowest RMSD of the ensemble was put back into MARDIGRAS for a second and third cycle of NOE calibration and structure calculations.	VnmrJ

NMR Ensemble Information
Conformer Selection Criteria	lowest RMSD to average structure
Conformers Calculated Total Number	50
Conformers Submitted Total Number	10
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	VnmrJ	2.1B	Varian
2	processing	NMRPipe	4.9	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3	chemical shift assignment	NMRView	8.0.b30	Johnson, One Moon Scientific
4	noe calibration	MARDIGRAS		T.L. James
5	structure solution	Amber	10	Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm
6	refinement	Amber	10	Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm
7	structure validation	CORMA		T.L. James