Seeing the Invisible: 50 Years of Macromolecular Visualization

Electron Density Maps: Relating the X-Ray Data Back to the Crystal

The measured spots of X-ray reflections need complex processing to be combined into a three-dimensional image of the molecule, called an electron density map.

Stacked sheets of isolated α-helix contours

Stacked sheets of isolated α-helix contours

Isolated α-helix contours
After the first model interpreted the helix, the lab made a clearer, simplified version of the stacked sheets for demo and teaching purposes, which omited all surrounding density and included only the helix itself.

Computer-displayed electron density contours

Computer-displayed electron density contours

Computer-displayed electron density contours
Modern methods are much better as well as easier to use, ever since the GRIP-75 system at UNC. Instead of multiple contour levels on separate layers, interactive computer displays show one or two density levels contoured in all three directions, to work as a three-dimensional object when the user zooms and rotates the view.

Computer contours, with model built in

Computer contours, with model built in

Computer contours, with model built in
The crystallographer's interpretation of the shapes to build an atomic model can be done right in place, as shown here. This is a small β-sheet of three extended strands held together by hydrogen bonds between backbone N (blue) and O (red) atoms, from the sulfate binding protein of PDB file 1sbp. Sidechains stick alternately up and down from a β-sheet, so most are outside this layer except the proline (Pro) and tyrosine (Tyr). Three classes of atoms are labeled: a , two backbone O atoms (carbonyl, or CO, oxygens) on adjacent strands, and a water oxygen in its isolated, round peak.