6FFR | pdb_00006ffr

DNA-RNA Hybrid Quadruplex with Flipped Tetrad

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 mixing time 500 ms	10 mM potassium phosphate, 0.48 mM DNA/RNA (5'-R(*G)-D(P*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*GP*AP*C)-R(P*G)-D(P*GP*G)-3')	90% H2O/10% D2O	10 mM	7	1 atm	298	Bruker AVANCE 600
2	2D 1H-1H NOESY mixing time 300 ms	10 mM potassium phosphate, 0.48 mM DNA/RNA (5'-R(*G)-D(P*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*GP*AP*C)-R(P*G)-D(P*GP*G)-3')	90% H2O/10% D2O	10 mM	7	1 atm	298	Bruker AVANCE 600
3	2D 1H-1H NOESY mixing time 150 ms	10 mM potassium phosphate, 0.48 mM DNA/RNA (5'-R(*G)-D(P*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*GP*AP*C)-R(P*G)-D(P*GP*G)-3')	90% H2O/10% D2O	10 mM	7	1 atm	298	Bruker AVANCE 600
4	2D 1H-1H NOESY mixing time 80 ms	10 mM potassium phosphate, 0.48 mM DNA/RNA (5'-R(*G)-D(P*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*GP*AP*C)-R(P*G)-D(P*GP*G)-3')	90% H2O/10% D2O	10 mM	7	1 atm	298	Bruker AVANCE 600
5	2D 1H-13C HSQC aromatic	10 mM potassium phosphate, 0.48 mM DNA/RNA (5'-R(*G)-D(P*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*GP*AP*C)-R(P*G)-D(P*GP*G)-3')	90% H2O/10% D2O	10 mM	7	1 atm	298	Bruker AVANCE 600
6	2D 1H-1H NOESY mixing time 300 ms	10 mM potassium phosphate, 0.48 mM DNA/RNA (5'-R(*G)-D(P*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*GP*AP*C)-R(P*G)-D(P*GP*G)-3')	100% D2O	10 mM	7	1 atm	298	Bruker AVANCE 600
7	2D 1H-13C HSQC aromatic	10 mM potassium phosphate, 0.48 mM DNA/RNA (5'-R(*G)-D(P*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*GP*AP*C)-R(P*G)-D(P*GP*G)-3')	100% D2O	10 mM	7	1 atm	298	Bruker AVANCE 600
8	2D DQF-COSY	10 mM potassium phosphate, 0.48 mM DNA/RNA (5'-R(*G)-D(P*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*GP*AP*C)-R(P*G)-D(P*GP*G)-3')	100% D2O	10 mM	7	1 atm	298	Bruker AVANCE 600
9	2D 1H-1H TOCSY	10 mM potassium phosphate, 0.48 mM DNA/RNA (5'-R(*G)-D(P*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*GP*AP*C)-R(P*G)-D(P*GP*G)-3')	100% D2O	10 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
DGSA-distance geometry simulated annealing		Xplor-NIH
simulated annealing		Amber

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

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	TopSpin	3.5	Bruker Biospin
2	chemical shift assignment	CcpNmr Analysis	2.4	CCPN
3	peak picking	CcpNmr Analysis	2.4	CCPN
4	refinement	Xplor-NIH	2.46	Schwieters, Kuszewski, Tjandra and Clore
5	structure calculation	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman