5B7J | pdb_00005b7j

Structure model of Sap1-DNA complex

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	0.5 mM [U-99% 15N][U-99% 13C; U-99% 15N] Sap1, 20 mM sodium phosphate	90% H2O/10% D2O	60 mM	6.0	1 atm	298	Bruker AVANCE 500
7	3D CBCA(CO)NH	0.5 mM [U-99% 15N][U-99% 13C; U-99% 15N] Sap1, 20 mM sodium phosphate	90% H2O/10% D2O	60 mM	6.0	1 atm	298	Bruker AVANCE 500
8	3D HNCACB	0.5 mM [U-99% 15N][U-99% 13C; U-99% 15N] Sap1, 20 mM sodium phosphate	90% H2O/10% D2O	60 mM	6.0	1 atm	298	Bruker AVANCE 500
12	3D HNCO	0.5 mM [U-99% 15N][U-99% 13C; U-99% 15N] Sap1, 20 mM sodium phosphate	90% H2O/10% D2O	60 mM	6.0	1 atm	298	Bruker AVANCE 500
9	2D 1H-15N HSQC	0.5 mM [U-99% 13C; U-99% 15N] Sap1, 0.7 mM DNA (5'-CAAAACAATATT-3'), 20 mM sodium phosphate	90% H2O/10% D2O	60 mM	6.0	1 atm	298	Bruker AVANCE 500
5	3D CBCA(CO)NH	0.5 mM [U-99% 13C; U-99% 15N] Sap1, 0.7 mM DNA (5'-CAAAACAATATT-3'), 20 mM sodium phosphate	90% H2O/10% D2O	60 mM	6.0	1 atm	298	Bruker AVANCE 500
6	3D HNCACB	0.5 mM [U-99% 13C; U-99% 15N] Sap1, 0.7 mM DNA (5'-CAAAACAATATT-3'), 20 mM sodium phosphate	90% H2O/10% D2O	60 mM	6.0	1 atm	298	Bruker AVANCE 500
10	3D HNCO	0.5 mM [U-99% 13C; U-99% 15N] Sap1, 0.7 mM DNA (5'-CAAAACAATATT-3'), 20 mM sodium phosphate	90% H2O/10% D2O	60 mM	6.0	1 atm	298	Bruker AVANCE 500
11	3D HNCA	0.5 mM [U-99% 13C; U-99% 15N] Sap1, 0.7 mM DNA (5'-CAAAACAATATT-3'), 20 mM sodium phosphate	90% H2O/10% D2O	60 mM	6.0	1 atm	298	Bruker AVANCE 500
2	3D 1H-15N NOESY	0.5 mM [U-99% 13C; U-99% 15N] Sap1, 0.7 mM DNA (5'-CAAAACAATATT-3'), 20 mM sodium phosphate	90% H2O/10% D2O	60 mM	6.0	1 atm	298	Bruker AVANCE 950
3	3D 1H-13C NOESY	0.5 mM [U-99% 13C; U-99% 15N] Sap1, 0.7 mM DNA (5'-CAAAACAATATT-3'), 20 mM sodium phosphate	90% H2O/10% D2O	60 mM	6.0	1 atm	298	Bruker AVANCE 950
13	3D filtered NOESY	0.5 mM [U-99% 13C; U-99% 15N] Sap1, 0.7 mM DNA (5'-CAAAACAATATT-3'), 20 mM sodium phosphate	90% H2O/10% D2O	60 mM	6.0	1 atm	298	Bruker AVANCE 950
4	2D 1H-1H NOESY	0.5 mM DNA (5'-CAAAACAATATT-3'), 20 mM sodium phosphate	90% H2O/10% D2O	60 mM	6.0	1 atm	298	Bruker AVANCE 950

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	500
2	Bruker	AVANCE	800
3	Bruker	AVANCE	950

NMR Refinement
Method	Details	Software
simulated annealing	The structure model of the Sap1-DNA complex was derived based on the crystal structure of Sap1, the B-form DNA model based on the 3D-DART server, and the experimentally obtained inter-molecular distance restraints from NMR NOESY spectra.	X-PLOR NIH

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	200
Conformers Submitted Total Number	20
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
2	refinement	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
3	chemical shift assignment	NMRView		Johnson, One Moon Scientific
4	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax