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Bending of the helical axis

Title		`CRYSTAL STRUCTURE OF A PAIRED DOMAIN-DNA COMPLEX AT 2.5 ANGSTROMS RESOLUTION REVEALS STRUCTURAL BASIS FOR PAX DEVELOPMENTAL MUTATIONS`
PDB code		`1PDN (PDB summary)`
NDB code		`PDR018 (NDB atlas)`
Duplex length		`13 base pairs`
Protein		`Paired protein, 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	0.053
Straight line (x-axis)	1.405
Arc	0.570	Radius of curvature: r = 86 Å
Kinked line	0.280	Kink angle: alpha = 18° Lengths of straight segments: l₁ = 5 bp, l₂ = 8 bp
Double kinked line	0.344	Kink angles: alpha₁ = 21°, alpha₂ = 8° Twist angle: omega = -153° Lengths of straight segments: l₁ = 5 bp, l₂ = 4 bp, l₃ = 3 bp