2MHZ | pdb_00002mhz

Structure of Exocyclic S,S N6,N6-(2,3-Dihydroxy-1,4-butadiyl)-2'-Deoxyadenosine Adduct Induced by 1,2,3,4-Diepoxybutane in DNA

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H NOESY	0.4 mM 5'-D(*CP*GP*GP*AP*CP*(SDE)P*AP*GP*AP*AP*G)-3', 0.4 mM 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3', 100 mM sodium chloride, 50 uM EDTA, 10 mM sodium phosphate	100% D2O	100	7	ambient	288
2	2D 1H-1H TOCSY	0.4 mM 5'-D(*CP*GP*GP*AP*CP*(SDE)P*AP*GP*AP*AP*G)-3', 0.4 mM 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3', 100 mM sodium chloride, 50 uM EDTA, 10 mM sodium phosphate	100% D2O	100	7	ambient	288
3	2D DQF-COSY	0.4 mM 5'-D(*CP*GP*GP*AP*CP*(SDE)P*AP*GP*AP*AP*G)-3', 0.4 mM 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3', 100 mM sodium chloride, 50 uM EDTA, 10 mM sodium phosphate	100% D2O	100	7	ambient	288
4	2D 1H-1H NOESY	0.4 mM 5'-D(*CP*GP*GP*AP*CP*(SDE)P*AP*GP*AP*AP*G)-3', 0.4 mM 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3', 100 mM sodium chloride, 50 uM EDTA, 10 mM sodium phosphate	90% H2O/10% D2O	100	7	ambient	278

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	800
2	Bruker	AVANCE	500

NMR Refinement
Method	Details	Software
molecular dynamics		Amber

NMR Ensemble Information
Conformer Selection Criteria	back calculated data agree with experimental NOESY spectrum
Conformers Calculated Total Number	8
Conformers Submitted Total Number	8
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	Amber		Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
2	data analysis	CORMA		Brandan A. Borgias, Paul D. Thomas, He Liu, Anil Kumar
3	conversion of intensities to distance restraints	MARDIGRAS		Brandan A. Borgias, Paul D. Thomas, He Liu, Anil Kumar, Marco Tonelli
4	chemical shift assignment	Sparky		Goddard
5	peak picking	Sparky		Goddard
6	chemical shift calculation	Sparky		Goddard
7	collection	TopSpin		Bruker Biospin
8	processing	TopSpin		Bruker Biospin
9	data analysis	Curves	plus web server	Christophe Blanchet, Marco Pasi, Krystyna Zakrzewska, Richard Lavery
10	refinement	Amber		Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman