Experiment: 1OSW

The Stem of SL1 RNA in HIV-1: Structure and Nucleocapsid Protein Binding for a 1X3 Internal Loop

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	1 mM SL1i RNA; 25mM NaCl, 5mM sodium phosphate, 0.1mM EDTA, 0.01% NaN3	99.996% D2O or 90% D2O, 10% H2O	25 mM NaCl	6.3	ambient	300
2	2D TOCSY	1 mM SL1i RNA; 25mM NaCl, 5mM sodium phosphate, 0.1mM EDTA, 0.01% NaN3	99.996% D2O or 90% D2O, 10% H2O	25 mM NaCl	6.3	ambient	300
3	HP-COSY	1 mM SL1i RNA; 25mM NaCl, 5mM sodium phosphate, 0.1mM EDTA, 0.01% NaN3	99.996% D2O or 90% D2O, 10% H2O	25 mM NaCl	6.3	ambient	300
4	2D NOESY	1 mM SL1i RNA; 25mM NaCl, 5mM sodium phosphate, 0.1mM EDTA, 0.01% NaN3	99.996% D2O or 90% D2O, 10% H2O	25 mM NaCl	5.5	ambient	278
5	H-C HSQC	1 mM SL1i RNA; 25mM NaCl, 5mM sodium phosphate, 0.1mM EDTA, 0.01% NaN3	99.996% D2O or 90% D2O, 10% H2O	25 mM NaCl	6.3	ambient	300

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	DRX	500
2	Bruker	DRX	600

NMR Refinement
Method	Details	Software
DYANA followed by molecular dynamics using AMBER		XwinNMR

NMR Ensemble Information
Conformer Selection Criteria	structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy,target function
Conformers Calculated Total Number	50
Conformers Submitted Total Number	23
Representative Model	17 (closest to the average)

Additional NMR Experimental Information
Details	Structures were determined using 2D NOESY at different temperatures and mixing times. The last residue, A23, was eliminated from the pdb file due to ambiguity in orientation.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	XwinNMR	2.6	Bruker
2	processing	NMRZ/TRIAD	6.1	Tripos
3	iterative matrix relaxation	MARDIGRAS	3.2	University of California, San Francisco
4	structure solution	DYANA	1.5	Guntert, P., Mumenthaler, C. and Wuthrich, K.
5	refinement	Amber	5.0	University of California, San Francisco