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Bending of the helical axis

Title STRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE DNA CLEAVAGE BY A RESTRICTION ENDONUCLEASE
PDB code 1BSU   (PDB summary)
NDB code PDE0145 (NDB atlas)
Duplex length 10 base pairs
Protein Restriction endonuclease EcoRV, 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  0.013  
 Straight line (x-axis) 6.419  
 Arc  0.567 Radius of curvature:  r = 21 Å
 Kinked line  0.050 Kink angle:  alpha = 50°
 Lengths of straight segments:  l1 = 5 bp,  l2 = 5 bp