DNA (5'-D(*GP*CP*GP*CP*GP*AP*AP*AP*CP*TP*GP*TP*TP*TP*CP*GP*CP*GP*C)-3')
Mass: 5821.759 Da / Num. of mol.: 1 / Fragment: FRAGMENT OF E2F BINDING DNA / Source method: obtained synthetically Details: The sequence is formed by adding CTG loop to ends of ds(GCGCGAAA:TTTCGCGC), which occurs naturally in humans.
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D NOESY
1
2
2
2D NOESY
NMR details
Text: Solvent suppression was realized by WATERGATE method.
Type: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz
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Processing
NMR software
Name
Version
Developer
Classification
XwinNMR
1.1
Bruker
collection
IRMA
0.1
AlexandreBonvin
iterativematrixrelaxation
GROMOS
96
W.F.vanGunsteren
refinement
Refinement
Method: Molecular Dynamics with Particle-Particle Particle-Mesh method; Iterative Relaxation Matrix Approach with generalized order parameters Software ordinal: 1 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 ...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
Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 2 / Conformers submitted total number: 2
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