6DM7 | pdb_00006dm7

NMR structure for Sp1 transcription factor duplex 5'-d(GGGGCGGGG)

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D DQF-COSY	1.0 mM DNA, 25 mM sodium chloride, 5 mM Na Phoshate, 0.5 mM EDTA	100% D2O	30 mM Na+ mM	7.0	1 atm	298	Bruker AVANCE 800
2	2D 1H-1H TOCSY	1.0 mM DNA, 25 mM sodium chloride, 5 mM Na Phoshate, 0.5 mM EDTA	100% D2O	30 mM Na+ mM	7.0	1 atm	298	Bruker AVANCE 800
3	2D 1H-13C HSQC	1.0 mM DNA, 25 mM sodium chloride, 5 mM Na Phoshate, 0.5 mM EDTA	100% D2O	30 mM Na+ mM	7.0	1 atm	298	Bruker AVANCE 800
4	2D 1H-1H NOESY	1.0 mM DNA, 25 mM sodium chloride, 5 mM Na Phoshate, 0.5 mM EDTA	100% D2O	30 mM Na+ mM	7.0	1 atm	298	Bruker AVANCE 800
5	2D 1H-1H NOESY	680 uM DNA, 25 mM sodium chloride, 5 mM Na Phosphate, 0.5 mM EDTA	90% H2O/10% D2O	30 mM Na+ mM	7.0	1 atm	298	Bruker AVANCE III 850
6	2D ECOSY	1.0 mM DNA, 25 mM sodium chloride, 5 mM Na Phoshate, 0.5 mM EDTA	100% D2O	30 mM Na+ mM	7.0	1 atm	298	Bruker AVANCE III 850
7	2D PhCOSY	1.0 mM DNA, 25 mM sodium chloride, 5 mM Na Phoshate, 0.5 mM EDTA	100% D2O	30 mM Na+ mM	7.0	1 atm	298	Bruker AVANCE II 600
8	2D PhTOCSY	1.0 mM DNA, 25 mM sodium chloride, 5 mM Na Phoshate, 0.5 mM EDTA	100% D2O	30 mM Na+ mM	7.0	1 atm	298	Bruker AVANCE II 600

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	800
3	Bruker	AVANCE III	850
2	Bruker	AVANCE II	600

NMR Refinement
Method	Details	Software
simulated annealing	214 NOE distance constraints, 54 hydrogen distance restraints, 48 dihedral angle restraints.	Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	20
Conformers Submitted Total Number	20
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	Amber	14.0	Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman
2	structure calculation	CYANA	3.97	Guntert, Mumenthaler and Wuthrich
3	chemical shift assignment	Sparky		Goddard
4	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
5	data analysis	3DNA		Lu
6	collection	TopSpin		Bruker Biospin