2LAR | pdb_00002lar

DNA / RNA Hybrid containing a central stereo specific Rp borano phosphate linkage

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	1.0 mM DNA (5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3'), 1.0 mM RNA (5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3'), 50 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA, 0.3 uM DSS	90% H2O/10% D2O	50	7.0	ambient	298
2	2D 1H-13C HSQC	1.0 mM DNA (5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3'), 1.0 mM RNA (5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3'), 50 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA, 0.3 uM DSS	99.999 % D2O	50	7.0	ambient	298
3	2D 1H-1H TOCSY	1.0 mM DNA (5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3'), 1.0 mM RNA (5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3'), 50 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA, 0.3 uM DSS	99.999 % D2O	50	7.0	ambient	298
4	2D DQF-COSY	1.0 mM DNA (5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3'), 1.0 mM RNA (5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3'), 50 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA, 0.3 uM DSS	99.999 % D2O	50	7.0	ambient	298
5	2D 1H-1H NOESY	1.0 mM DNA (5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3'), 1.0 mM RNA (5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3'), 50 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA, 0.3 uM DSS	99.999 % D2O	50	7.0	ambient	298
6	2D 1H-31P CORR	1.0 mM DNA (5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3'), 1.0 mM RNA (5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3'), 50 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA, 0.3 uM DSS	99.999 % D2O	50	7.0	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	600
2	Bruker	AVANCE	500

NMR Refinement
Method	Details	Software
molecular dynamics, matrix relaxation		Amber

NMR Ensemble Information
Conformer Selection Criteria	structure with the lowest restraint violations
Conformers Calculated Total Number	10
Conformers Submitted Total Number	1
Representative Model	1 (structure with the lowest restraint violations)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	Amber	9.0	Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm
2	geometry optimization	Amber	9.0	Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm
3	refinement	Amber	9.0	Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm
4	collection	XwinNMR	3.5	Bruker Biospin
5	data analysis	TopSpin	2.1	Bruker Biospin
6	chemical shift calculation	TopSpin	2.1	Bruker Biospin
7	processing	TopSpin	2.1	Bruker Biospin
8	data analysis	CORMA	5.21	(CORMA) Dr. Thomas James
9	refinement	MARDIGRAS	5.21	Thomas James
10	data analysis	Sparky	3.98	Goddard
11	chemical shift assignment	Sparky	3.98	Goddard