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Bending of the helical axis

Title		`3D SOLUTION NMR STRUCTURE OF THE WILD TYPE HMG-BOX DOMAIN OF THE HUMAN MALE SEX DETERMINING FACTOR SRY COMPLEXED TO DNA`
PDB code		`1J46 (PDB summary)`
NDB code		`1J46 (NDB atlas)`
Duplex length		`14 base pairs`
Protein		`Human male sex-determining factor SRY, hSRY(HMG), Transcription Factor, DNA binding domain: High mobility group`

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	0.033
Straight line (x-axis)	8.243
Arc	0.335	Radius of curvature: r = 38 Å
Kinked line	0.291	Kink angle: alpha = 40° Lengths of straight segments: l₁ = 8 bp, l₂ = 6 bp
Double kinked line	0.278	Kink angles: alpha₁ = 13°, alpha₂ = 34° Twist angle: omega = 4° Lengths of straight segments: l₁ = 4 bp, l₂ = 5 bp, l₃ = 5 bp