1P96 | pdb_00001p96

Solution Structure of a Wedge-Shaped Synthetic Molecule at a Two-Base Bulge Site in DNA

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	1.8mM DDI-bulged DNA complex, 0.1M NaCl, 10mM sodium phosphate and 0.1mM EDTA buffer,90% H20/10% D20; 99.96% D20	90% H20/10% D20; 99.96% D20	0.1M NaCl, 10mM sodium phosphate, 0.1mM EDTA	6.5	ambient	298
2	2D TOCSY	1.8mM DDI-bulged DNA complex, 0.1M NaCl, 10mM sodium phosphate and 0.1mM EDTA buffer,90% H20/10% D20; 99.96% D20	90% H20/10% D20; 99.96% D20	0.1M NaCl, 10mM sodium phosphate, 0.1mM EDTA	6.5	ambient	298
3	DQF-COSY	1.8mM DDI-bulged DNA complex, 0.1M NaCl, 10mM sodium phosphate and 0.1mM EDTA buffer,90% H20/10% D20; 99.96% D20	90% H20/10% D20; 99.96% D20	0.1M NaCl, 10mM sodium phosphate, 0.1mM EDTA	6.5	ambient	298
4	H-P COSY	1.8mM DDI-bulged DNA complex, 0.1M NaCl, 10mM sodium phosphate and 0.1mM EDTA buffer,90% H20/10% D20; 99.96% D20	90% H20/10% D20; 99.96% D20	0.1M NaCl, 10mM sodium phosphate, 0.1mM EDTA	6.5	ambient	298
5	COSY-45	1.8mM DDI-bulged DNA complex, 0.1M NaCl, 10mM sodium phosphate and 0.1mM EDTA buffer,90% H20/10% D20; 99.96% D20	90% H20/10% D20; 99.96% D20	0.1M NaCl, 10mM sodium phosphate, 0.1mM EDTA	6.5	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	600
2	Varian	INOVA	750
3	Varian	INOVA	500

NMR Refinement
Method	Details	Software
distance geometry sinulated annealing	The structures are based on a total of 694 NOE restranints and 166 dihedral angle restraints.	NMRPipe

NMR Ensemble Information
Conformer Selection Criteria	all calculated structures submitted
Conformers Calculated Total Number	10
Conformers Submitted Total Number	10
Representative Model	1 (all calculated structures submited have the least restraint violation and the lowst energy.)

Additional NMR Experimental Information
Details	This structure was determined using 2D homonuclear and heteronuclear techniques.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	NMRPipe	2002.044.17.08	Delaglio, F.
2	data analysis	Sparky	3.106	Goddard, T.D. and Kneller, D.G.
3	refinement	CNS	1.0	Brunger, A.T. 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.