1S0T

Solution structure of a DNA duplex containing an alpha-anomeric adenosine: insights into substrate recognition by endonuclease IV

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	1.0 mM alphaA duplex, 10 mM phosphate buffer, 50 mM NaCl, 0.1 mM EDTA, pH 6.6	100% D2O	50 mM NaCl	6.6	ambient	293
2	DQF-COSY	1.0 mM alphaA duplex, 10 mM phosphate buffer, 50 mM NaCl, 0.1 mM EDTA, pH 6.6	100% D2O	50 mM NaCl	6.6	ambient	293
3	2D TOCSY	1.0 mM alphaA duplex, 10 mM phosphate buffer, 50 mM NaCl, 0.1 mM EDTA, pH 6.6	100% D2O	50 mM NaCl	6.6	ambient	293
4	2D 31P,1H correlation	1.0 mM alphaA duplex, 10 mM phosphate buffer, 50 mM NaCl, 0.1 mM EDTA, pH 6.6	100% D2O	50 mM NaCl	6.6	ambient	293
5	HSQC	1.0 mM alphaA duplex, 10 mM phosphate buffer, 50 mM NaCl, 0.1 mM EDTA, pH 6.6	100% D2O	50 mM NaCl	6.6	ambient	293

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AMX	600
2	Bruker	AVANCE	500

NMR Refinement
Method	Details	Software
torsion angle dynamics molecular dynamics	The structure is based on a total of 502 restraints: 284 distance restraints, 80 endocyclic torsion angle restraints, 50 Watson-Crick distance and angle restraints, and 88 backbone torsion angle restraints. The alphaA duplex structure was elucidated by a combination of DYANA and rMD/rEM in AMBER. All calculations were performed in vacuo. The final structure deposited here was obtained by coordinate averaging the final ensemble of 10 rMD/rEM structures followed by restrained energy minimization.	DYANA

NMR Ensemble Information
Conformer Selection Criteria
Conformers Calculated Total Number	10
Conformers Submitted Total Number	1
Representative Model	1 (minimized average structure)

Additional NMR Experimental Information
Details	For non-exchangeable protons, NOESY experiments in D2O were performed with 10s relaxation delays and mixing times of 75ms, 150ms and 250 ms. For exchangeable protons, a WATERGATE NOESY was performed with a relaxation delay of 4s and 150ms mixing time.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	DYANA	1.5	Guntert et al
2	refinement	Amber	6.0	Case et al.
3	iterative matrix relaxation	MARDIGRAS	3.2	Borgias et al.
4	structure solution	CORMA	5.2	Keepers and James
5	structure solution	Curves	5.1	Lavery and Sklenar
6	structure solution	MOLMOL	2.0	Koradi 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 R01GM133198.