SOLUTION NMR Experimental Data


Experimental Details
Sample Conditions
Sample Contents3.5mM DNA fragment; 50mM phosphate buffer, pH 7.0; 150mM NaCl; 1mM EDTA; 1mM NaN3; 90% H2O, 10% D2O
Solvent90% H2O/10% D2O
Ionic Strength150mM NaCl
pH7.0
Pressureambient
Temperature (K)300
Experiment(s):2D NOESY
Sample Contentssame as 1 except in D2O
Solvent99.96% D2O
Ionic Strength150mM NaCl
pH7.0
Pressureambient
Temperature (K)300
Experiment(s):2D NOESY
Spectrometer Information
Manufacturer Model Field Strength
Bruker DMX 500.0
NMR Refinement
Method Molecular Dynamics with Particle-Particle Particle-Mesh method; Iterative Relaxation Matrix Approach with generalized order parameters
Details 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
NMR Ensemble Information
Conformer Selection Criteria all calculated structures submitted
Conformers Calculated Total Number 2
Conformers Submitted Total Number 2
Additional NMR Experimental Information
1 Solvent suppression was realized by WATERGATE method.
Computation: NMR Software
# Classification Software Name Author
1 collection version: 1.1 XWINNMR Bruker
2 iterative matrix relaxation version: 0.1 IRMA Alexandre Bonvin
3 refinement version: 96 GROMOS W.F.van Gunsteren