7NBL | pdb_00007nbl

Solution structure of DNA:RNA hybrid containing a 2'-deoxy-2'2'-difluorodeoxycytidine (gemcitabine) modification

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	0.5 M DNA (5'-D(*CP*TP*AP*(FFC)P*AP*CP*GP*G)-3'), 0.5 M RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 0.5 % v/v DSS	90% H2O/10% D2O	125 mM	7	1 atm	278	Bruker AVANCE 600
2	2D 1H-1H TOCSY	0.5 M DNA (5'-D(*CP*TP*AP*(FFC)P*AP*CP*GP*G)-3'), 0.5 M RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 0.5 % v/v DSS	90% H2O/10% D2O	125 mM	7	1 atm	278	Bruker AVANCE 600
3	2D 1H-1H COSY	0.5 M DNA (5'-D(*CP*TP*AP*(FFC)P*AP*CP*GP*G)-3'), 0.5 M RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 0.5 % v/v DSS	100% D2O	125 mM	7	1 atm	298	Bruker AVANCE 600
4	2D 1H-1H NOESY	0.5 M DNA (5'-D(*CP*TP*AP*(FFC)P*AP*CP*GP*G)-3'), 0.5 M RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 0.5 % v/v DSS	100% D2O	125 mM	7	1 atm	298	Bruker AVANCE 600
5	2D 1H-1H TOCSY	0.5 M DNA (5'-D(*CP*TP*AP*(FFC)P*AP*CP*GP*G)-3'), 0.5 M RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 0.5 % v/v DSS	100% D2O	125 mM	7	1 atm	298	Bruker AVANCE 600

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	600

NMR Refinement
Method	Details	Software
molecular dynamics		Amber

NMR Ensemble Information
Conformer Selection Criteria	all calculated structures submitted
Conformers Calculated Total Number	10
Conformers Submitted Total Number	10
Representative Model	1 (fewest violations)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin		Bruker Biospin
2	processing	TopSpin		Bruker Biospin
3	chemical shift assignment	NMRFAM-SPARKY		Goddard & Kneller
4	structure calculation	Amber	18	Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
5	refinement	Amber	18	Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
6	data analysis	MOLMOL		Koradi, Billeter and Wuthrich
7	data analysis	3DNA		Lu & Olson