Sigma level crystallography

  • What does Sigma mean in crystallography?

    Sigma: a common shorthand term for standard deviation.
    May occur in several contexts in macromolecular crystallography, most commonly referring to the sigma-scaling of maps.
    Sigma-A weighting: a method of weighting difference map coefficients to more accurately account for errors in the model..

  • What is the difference between 2Fo-FC and fo-FC?

    The .

    1. Fo-Fc map represents the electron densities surrounding well-determined atoms in the model across a three-dimensional (
    2. D) space and the Fo-Fc map represents the electron density discrepancies between the observed and calculated electron density across a
    3. D space

  • What is the sigma level of 2Fo-FC?

    For .

    1. Fo-Fc maps the most suitable sigma level is 1
      2. . (It could be higher when contouring an electron-rich area, such as a heavy atom site, but not lower.) Fo-Fc maps are typically contoured at + or - 2.5sigma.

The "sigma level" you're referring to is the contour level or cut-off point in the intensity of any particular 3D representation of the electron density 

How accurate is a macromolecular crystallography map?

In both cryo-EM and in macromolecular crystallography, the accuracy of the map is an important characteristic

In macromolecular crystallography, the amplitudes of Fourier coefficients are generally measured accurately and the phases are poorly estimated

What are the direct results of crystallographic experiments?

The direct results of crystallographic experiments are electron density maps

The atomic model is the authors' interpretation of the map

Examining the correspondence between the electron density map and the published molecular model reveals regions of uncertainty in the model

2Why Look At Electron Density Maps?

What is a sigma level in a topographical map?

Typically the peaks in the F o – F c map are colored green and the minima are colored red

The sigma level is an estimate of the noise in the map, and is analogous to setting a minimum elevation on a topographical map, such that only peaks above a certain threshold are drawn

An X-ray crystallographic experiment produces anelectron density mapfor the averageunit cellof the protein

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