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Bending of the helical axis

Title CRYSTAL STRUCTURE OF TRANSCRIPTION ACTIVATOR BMRR, FROM B. S BOUND TO 21 BASE PAIR BMR OPERATOR AND TPSB
PDB code 1EXI   (PDB summary)
NDB code PD0145 (NDB atlas)
Duplex length 21 base pairs
Protein BmrR, 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  0.279  
 Straight line (x-axis) 9.879  
 Arc  1.783 Radius of curvature:  r = 64 Å
 Kinked line  0.533 Kink angle:  alpha = 33°
 Lengths of straight segments:  l1 = 10 bp,  l2 = 10 bp  
 Double kinked line  0.285 Kink angles:  alpha1 = 93°,  alpha2 = 92°  
 Twist angle:  omega = -147°  
 Lengths of straight segments:  l1 = 10 bp,  l2 = 1 bp,  l3 = 10 bp  
The length of the central segments of the double kinked line is 1 bp. Segments 1 and 3 should be interpreted as two warped lines. See Help for further explanations.