2KYD | pdb_00002kyd

RDC and RCSA refinement of an A-form RNA: Improvements in Major Groove Width

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	0.25-1 mM RNA, 0.25 mM [U-100% 13C], [C-100% 13C] RNA, 0.25 mM [G-100% 13C], [A-100% 13C] RNA, 150 mM sodium chloride, 10 mM TRIS	100% D2O	0.15	6.5	ambient	303
2	2D 1H-1H TOCSY	0.25-1 mM RNA, 0.25 mM [U-100% 13C], [C-100% 13C] RNA, 0.25 mM [G-100% 13C], [A-100% 13C] RNA, 150 mM sodium chloride, 10 mM TRIS	100% D2O	0.15	6.5	ambient	303
3	2D 1H-13C HMQC	0.25-1 mM RNA, 0.25 mM [U-100% 13C], [C-100% 13C] RNA, 0.25 mM [G-100% 13C], [A-100% 13C] RNA, 150 mM sodium chloride, 10 mM TRIS	100% D2O	0.15	6.5	ambient	303
4	2D Tr 1H-13C HSQC	0.25-1 mM RNA, 0.25 mM [U-100% 13C], [C-100% 13C] RNA, 0.25 mM [G-100% 13C], [A-100% 13C] RNA, 150 mM sodium chloride, 10 mM TRIS	100% D2O	0.15	6.5	ambient	303
5	2D Tr 1H-13C HSQC	0.25-1 mM RNA, 0.25 mM [U-100% 13C], [C-100% 13C] RNA, 0.25 mM [G-100% 13C], [A-100% 13C] RNA, 150 mM sodium chloride, 10 mM TRIS	100% D2O	0.15	6.5	ambient	303

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	800
2	Bruker	DMX	600

NMR Refinement
Method	Details	Software
molecular dynamics		Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with the least restraint violations
Conformers Calculated Total Number	200
Conformers Submitted Total Number	20
Representative Model	1 (fewest violations)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	Amber		Case, D. et al.
2	geometry optimization	CYANA		Guntert, P. et al.