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Bending of the helical axis

Title		`PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYS STRUCTURES OF CAP-DNA COMPLEXES`
PDB code		`1O3T (PDB summary)`
NDB code		`PD0401 (NDB atlas)`
Duplex length		`13 base pairs`
Protein		`Catabolite gene activator, Transcription Factor, DNA binding domain: Alpha-helix, DNA binding domain: Helix-turn-helix`

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	0.103
Straight line (x-axis)	5.136
Arc	0.789	Radius of curvature: r = 44 Å
Kinked line	0.506	Kink angle: alpha = 34° Lengths of straight segments: l₁ = 5 bp, l₂ = 8 bp
Double kinked line	0.306	Kink angles: alpha₁ = 36°, alpha₂ = 12° Twist angle: omega = 51° Lengths of straight segments: l₁ = 3 bp, l₂ = 4 bp, l₃ = 6 bp