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Bending of the helical axis

Title STRUCTURE OF THE HOMEOTIC UBX/EXD/DNA TERNARY COMPLEX
PDB code 1B8I   (PDB summary)
NDB code PD0042 (NDB atlas)
Duplex length 13 base pairs
Protein Ultrabithorax-extradenticle heterodimer, Transcription factor, DNA binding domain: Helix-turn-helix, homeodomain


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  0.057  
 Straight line (x-axis) 1.425  
 Arc  0.205 Radius of curvature:  r = 74 Å
 Kinked line  0.173 Kink angle:  alpha = 18°
 Lengths of straight segments:  l1 = 7 bp,  l2 = 6 bp  
 Double kinked line  0.299 Kink angles:  alpha1 = 5°,  alpha2 = 16°  
 Twist angle:  omega = 34°  
 Lengths of straight segments:  l1 = 3 bp,  l2 = 5 bp,  l3 = 5 bp