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Bending of the helical axis

Title X-RAY STRUCTURE OF THE DNA-ECO RI ENDONUCLEASE-DNA RECOGNITION COMPLEX: THE RECOGNITION NETWORK AND THE INTEGRATION OF RECOGNITION AND CLEAVAGE
PDB code 1ERI   (PDB summary)
NDB code PDE001 (NDB atlas)
Duplex length 12 base pairs
Protein Restriction endonuclease EcoRI, Nuclease

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  0.034  
 Straight line (x-axis) 0.163  
 Arc  0.217 Radius of curvature:  r = 232000000 Å
 Kinked line  0.260 Kink angle:  alpha = ill defined
 Lengths of straight segments:  l1 = 12 bp,  l2 = 0 bp