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Bending of the helical axis

Title CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I FRAGMENT PROD COMPLEX WITH 12 BASE PAIRS OF DUPLEX DNA FOLLOWING ADDITION DTTP, A DATP, AND A DCTP RESIDUE.
PDB code 1L5U   (PDB summary)
NDB code PD0304 (NDB atlas)
Duplex length 12 base pairs
Protein DNA POLYMERASE I KLENOW FRAGMENT, Polymerase

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  0.056  
 Straight line (x-axis) 0.449  
 Arc  0.158 Radius of curvature:  r = 116 Å
 Kinked line  0.127 Kink angle:  alpha = 10°
 Lengths of straight segments:  l1 = 5 bp,  l2 = 6 bp