An Omit Map of the Active Site of Malate Synthase

     In this figure, you can see the electron density surrounding the magnesium coordination sphere.  This map was calculated after refining the structure in the absence of these atoms, before calculation of a difference map.  A difference map or an Fo-Fc map shows the electron density in regions where the density is stronger than what would be expected from the model alone.  Positive peaks in a difference map show where there is additional electron density that needs to be explained.  This technique is used in model building to obtain a relatively unbiased view of the electron density in regions where the model has been omitted and to verify the occupancy of atoms in the model.  The electon density is contoured as a blue wire cage surrounding the atomic coordinates of the final refined model.  The magnesium is purple, carbons green and oxygens red.  Metal-oxygen bonds are shown in black, while other bonds are shown in yellow.  Glyoxylate is on the left, Aspartate 455 on the right and Glutamate 427 below.  The oxygen atom in front and the one at the top represent water molecules.  Hydrogen atoms are not included due to the resolution limits of the observed data.