Biochemistry I Map Fitting in X-Ray Diffraction
 
  Suggestions for Use:
The buttons in the left column will generate a poly-alanine chain.
The middle set of buttons will zoom in on the indicated residue, the b-carbon is colored purple.
The right set of buttons adds the sidechain. The sequence of this segment of the protein is:
    Gly61-Phe62-Gly63-Phe64-Leu65-Arg66-Ser67
Growing PolyAla
Chain (N-->C)		 Individual
Residues  
C b, colored purple		 Placement of
Side Chains
           
           
           
           
           
           
           
        
 

The electron density map1 associated with a short segment (residues 61-67) of a b-stand within a protein is shown. This 'chicken-wire' representation indicates which regions of space have high electron density (inside the chicken wire) or low electron density (outside the cage.)
  The crystallographer places the correct residue into the cage based on the electron density. The mainchain atoms are usually built into the electron density first as a polyalanine chain, followed by placement of the side-chains. The placement of the side-chains is guided by the known primary structure of the protein.

1The electron density map is obtained by Fourier transformation of the scattered X-rays. In this particular illustration the molecular surface is shown instead, as calculated with M.L. Connolly's surface program (Science 221, 709-713.)