2K71 | pdb_00002k71

Structure and dynamics of a DNA GNRA hairpin solved vy high-sensitivity NMR with two independent converging methods, simulated annealing (DYANA) and mesoscopic molecular modelling (BCE/AMBER)

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D DQF-COSY	4 mM dGCGAAAGC, 10 mM sodium phosphate, 0.0025 mM sodium azide, 0.005 mM EDTA, 50 mM sodium chloride	100% D2O	50	6.8	ambient	298
2	2D 1H-13C HSQC	4 mM dGCGAAAGC, 10 mM sodium phosphate, 0.0025 mM sodium azide, 0.005 mM EDTA, 50 mM sodium chloride	100% D2O	50	6.8	ambient	298
3	2D 1H-31P COSY	4 mM dGCGAAAGC, 10 mM sodium phosphate, 0.0025 mM sodium azide, 0.005 mM EDTA, 50 mM sodium chloride	100% D2O	50	6.8	ambient	298
4	2D 1H-1H NOESY	4 mM dGCGAAAGC, 10 mM sodium phosphate, 0.0025 mM sodium azide, 0.005 mM EDTA, 50 mM sodium chloride	100% D2O	50	6.8	ambient	298
5	2D 1H-1H NOESY	4 mM dGCGAAAGC, 10 mM sodium phosphate, 0.0025 mM sodium azide, 0.005 mM EDTA, 50 mM sodium chloride	90% H2O/10% D2O	50	6.8	ambient	274

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	750
2	Varian	UNITY	400

NMR Refinement
Method	Details	Software
simulated annealing, Biopolymer Chain Elasticity approach	100 structures were used in DYANA simulated annealing approach to give models 1 to 20 that were energy-refined with AMBER, Model number 21 was constructed with the BCE approach in agreement with the NMR data and then energy-refined with AMBER	VNMR

NMR Ensemble Information
Conformer Selection Criteria	structures with the least restraint violations
Conformers Calculated Total Number	101
Conformers Submitted Total Number	21
Representative Model	1 (fewest violations)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	VNMR		Varian
2	data analysis	PROSA		Guntert
3	refinement	DYANA		Guntert, Braun and Wuthrich
4	structure solution	DYANA		Guntert, Braun and Wuthrich
5	visualisation	MOLMOL		Koradi, Billeter and Wuthrich