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NMR STRUCTURE OF THE DIMER INITIATION COMPLEX OF HIV-1 GENOMIC RNA, MINIMIZED AVERAGE STRUCTURE
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
2D NOE IN D2O
D2O AND H2O
100 mM NACL
6.4
298
2
2D NOE IN WATER
D2O AND H2O
100 mM NACL
6.4
298
3
DQF-COSY
D2O AND H2O
100 mM NACL
6.4
298
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Varian
UNITYPLUS
600
NMR Refinement
Method
Details
Software
RANDOMLY GENERATED STRUCTURES WERE FOLDED IN DYANA USING NMR DRIVEN STRUCTURAL RESTRAINTS. 34 STRUCTURES SHOWING LOWEST TARGET FUNCTION VALUES AND NO CONSISTENT VIOLATIONS OF NMR RESTRAINTS WERE INDIVIDUALLY SUBJECTED TO RESTRAINED ENERGY MINIMIZATION IN AMBER 4.1. FOR DETAILS OF REFINEMENT PROTOCOL, PLEASE REFER TO THE REFERENCE ABOVE.
DYANA
NMR Ensemble Information
Conformer Selection Criteria
LOWEST NMR CONSTRAINT VIOLATIONS AND LOWEST AMBER ENERGY.
Conformers Calculated Total Number
34
Conformers Submitted Total Number
1
Additional NMR Experimental Information
Details
INTERPROTON-DISTANCE INFORMATION (IN THE FORM OF NOE CROSS-PEAKS) WAS COLLECTED FROM 2D NOE EXPERIMENTS IN D2O AS WELL AS IN 90% H2O FOR NON-EXCHANGEABLE AND EXCHANGEABLE PROTONS, RESPECTIVELY. 2D NOE EXPERIMENTS WERE CARRIED OUT AT 50, 80, 200 AND 400 M SEC MIXING TIMES. COUPLING CONSTANTS AND SUGAR CONFORMATIONS WERE DEDUCED FROM DQF-COSY EXPERIMENTS.