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Bending of the helical axis

Title		`CRYSTAL STRUCTURE OF A TRAPPED REACTION INTERMEDIATE OF THE ENZYME ENDONUCLEASE VIII WITH DNA`
PDB code		`1K3W (PDB summary)`
NDB code		`PD0253 (NDB atlas)`
Duplex length		`18 base pairs`
Protein		`Endonuclease VIII (EC 3.2.-.-), Nuclease\|repair, DNA binding domain: UDG\|alpha-helix\|beta-barrel`

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	0.069
Straight line (x-axis)	11.971
Arc	1.044	Radius of curvature: r = 42 Å
Kinked line	0.328	Kink angle: alpha = 42° Lengths of straight segments: l₁ = 8 bp, l₂ = 10 bp
Double kinked line	0.218	Kink angles: alpha₁ = 19°, alpha₂ = 30° Twist angle: omega = 2° Lengths of straight segments: l₁ = 5 bp, l₂ = 4 bp, l₃ = 9 bp