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Bending of the helical axis

Title CRYSTAL STRUCTURE OF THE NC2-TBP-DNA TERNARY COMPLEX
PDB code 1JFI   (PDB summary)
NDB code PD0221 (NDB atlas)
Duplex length 17 base pairs
Protein H2A/H2B, Tbp, Transcription Factor


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  1.192  
 Straight line (x-axis) 17.419  
 Arc  1.756 Radius of curvature:  r = 28 Å
 Kinked line  2.634 Kink angle:  alpha = 54°
 Lengths of straight segments:  l1 = 8 bp,  l2 = 9 bp  
 Double kinked line  0.508 Kink angles:  alpha1 = 41°,  alpha2 = 39°  
 Twist angle:  omega = 68°  
 Lengths of straight segments:  l1 = 7 bp,  l2 = 4 bp,  l3 = 6 bp