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Bending of the helical axis

Title DIMER INITIATION SEQUENCE OF HIV-1LAI GENOMIC RNA: NMR SOLUTION STRUCTURE OF THE EXTENDED DUPLEX
PDB code 1JU1   (PDB summary)
NDB code 1JU1 (NDB atlas)
Duplex length 23 base pairs


Table 1.   Bending parameters determined with the program ARC_FIT.  
The curvilinear helical axis is calculated with CURVES, and bending of this axis is analysed with ARC_FIT. This program allows to fit a straight line, a plane, an arc, a kinked line, and a double kinked line to the helical axis. Good fits are indicated by low values of sigma2. An arc is fitted if there are at least 7 bp. A kinked line requires at least 8 bp, and the double kinked line requires at least 13 bp. The geometrical parameters are given for all models fitted, but they characterize the shape of the helical axis only if the fit is good. See Help for further explanations.

 Model      sigma2 / Å2   Geometrical parameters 
 Plane  0.876  
 Straight line (x-axis) 5.979  
 Arc  6.683 Radius of curvature:  r = 904000000 Å
 Kinked line  3.841 Kink angle:  alpha = 35°
 Lengths of straight segments:  l1 = 5 bp,  l2 = 18 bp  
 Double kinked line  3.481 Kink angles:  alpha1 = 32°,  alpha2 = 32°  
 Twist angle:  omega = -21°  
 Lengths of straight segments:  l1 = 5 bp,  l2 = 15 bp,  l3 = 3 bp