8ZD7 | pdb_00008zd7

NMR structure of the CGG-dsDNA-sND complex

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	2.0 mM None DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*G)-3'), 2.0 mM None DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3'), 2.0 mM None sND, 20 mM None sodium phosphate (pH 6.8), 100 mM None NaCl	95% H2O/5% D2O	120 mM	6.8	1 atm	303	Bruker AVANCE III HD 800
2	2D 1H-1H TOCSY	2.0 mM None DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*G)-3'), 2.0 mM None DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3'), 2.0 mM None sND, 20 mM None sodium phosphate (pH 6.8), 100 mM None NaCl	95% H2O/5% D2O	120 mM	6.8	1 atm	303	Bruker AVANCE III HD 800
3	2D 1H-1H DQF-COSY	2.0 mM None DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*G)-3'), 2.0 mM None DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3'), 2.0 mM None sND, 20 mM None sodium phosphate (pH 6.8), 100 mM None NaCl	95% H2O/5% D2O	120 mM	6.8	1 atm	303	Bruker AVANCE III HD 800
4	2D 1H-31P HSQC	2.0 mM None DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*G)-3'), 2.0 mM None DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3'), 2.0 mM None sND, 20 mM None sodium phosphate (pH 6.8), 100 mM None NaCl	95% H2O/5% D2O	120 mM	6.8	1 atm	303	Bruker AVANCE III HD 600
5	2D 1H-13C HSQC	2.0 mM None DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*G)-3'), 2.0 mM None DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3'), 2.0 mM None sND, 20 mM None sodium phosphate (pH 6.8), 100 mM None NaCl	95% H2O/5% D2O	120 mM	6.8	1 atm	303	Bruker AVANCE III HD 800
6	2D 1H-15N HSQC	2.0 mM None DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*G)-3'), 2.0 mM None DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3'), 2.0 mM None sND, 20 mM None sodium phosphate (pH 6.8), 100 mM None NaCl	95% H2O/5% D2O	120 mM	6.8	1 atm	303	Bruker AVANCE III 950
7	2D 1H-13C HSQC	2.0 mM None DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*G)-3'), 2.0 mM None DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3'), 2.0 mM None sND, 20 mM None sodium phosphate (pH 6.8), 100 mM None NaCl, 12 mg/mL None Pf1	95% H2O/5% D2O	120 mM	6.8	1 atm	303	Bruker AVANCE III HD 800

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III	950
2	Bruker	AVANCE III HD	800
3	Bruker	AVANCE III HD	600
4	Bruker	AVANCE III HD	500

NMR Refinement
Method	Details	Software
simulated annealing	RDC was used for refinement	CNS

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	150
Conformers Submitted Total Number	30
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	chemical shift assignment	NMRFAM-SPARKY		Lee W, Tonelli M, Markley JL
2	structure calculation	CNS		Brunger, Adams, Clore, Gros, Nilges and Read
3	refinement	CNS		Brunger, Adams, Clore, Gros, Nilges and Read
4	peak picking	NMRFAM-SPARKY		Lee W, Tonelli M, Markley JL
5	processing	TopSpin		Bruker Biospin