Advanced Methods in Structural Biology by Toshiya Senda & Katsumi Maenaka

Author:Toshiya Senda & Katsumi Maenaka
Language: eng
Format: epub
Publisher: Springer Japan, Tokyo

2.Specify the meniscus, bottom position, and fitting limits. Set meniscus (red line) to the midpoint position of the absorbance spike corresponding to the air–sample boundary. Set the bottom position (blue line) to the maximum signal corresponding to optical artifacts at the end of the solution column. Set the left and right data analysis limits (green lines) to exclude the region of optical artifacts close to the meniscus and bottom.

3.Choose continuous C(s) distribution from the “Model” menu. In the “Parameter” box, input the minimum (smin) and maximum (smax) expected sedimentation coefficient values. Input the resolution. This parameter corresponds to the number of species with different s-values between smin and smax in which relative abundance will be determined in the C(s) analysis. Input the initial value for the frictional ratio: 1.2 for globular proteins, 1.5 for antibodies or other asymmetrically shaped proteins, and 2.0 or higher for rod-shaped and unfolded proteins, fibrils, and DNA. Input the values for partial specific volume (vbar), solvent density, and viscosity. Set the confidence level to 0.68. Check the boxes for the frictional ratio, baseline, meniscus, and time-independent noise (and radial-independent (RI) noise when interference optics is used for the data acquisition) in order to optimize these parameters.

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