1ECU | pdb_00001ecu

SOLUTION STRUCTURE OF E2F BINDING DNA FRAGMENT GCGCGAAAC-T-GTTTCGCGC

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	3.5mM DNA fragment; 50mM phosphate buffer, pH 7.0; 150mM NaCl; 1mM EDTA; 1mM NaN3; 90% H2O, 10% D2O	90% H2O/10% D2O	150mM NaCl	7.0	ambient	300
2	2D NOESY	same as 1 except in D2O	99.96% D2O	150mM NaCl	7.0	ambient	300

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	DMX	500

NMR Refinement
Method	Details	Software
Molecular Dynamics with Particle-Particle Particle-Mesh method; Iterative Relaxation Matrix Approach with generalized order parameters	Initial structure for model 1 is A-DNA, while that for model 2 is B-DNA. First we applied 640ps free MD with 18 Na+ counterions and 2789 waters for A-DNA and 2303 waters for B-DNA. Then we applied 4 cycles of IRMA with 174 NOE restraints and 19 hydrogen bond restraints	XwinNMR

NMR Ensemble Information
Conformer Selection Criteria	all calculated structures submitted
Conformers Calculated Total Number	2
Conformers Submitted Total Number	2

Additional NMR Experimental Information
Details	Solvent suppression was realized by WATERGATE method.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	XwinNMR	1.1	Bruker
2	iterative matrix relaxation	IRMA	0.1	Alexandre Bonvin
3	refinement	GROMOS	96	W.F.van Gunsteren

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.