Electron density maps
85% of the macromolecular structures available from the Protein_Data_Bank (PDB) were determined by X-ray_crystallography. A crystallographic experiment produces an electron density map for the average unit cell of the protein crystal. The amino acid (or nucleotide) sequence of the crystallized polymer(s) is known in advance. The crystallographer fits the atoms of the known molecules into the electron density map, and refines the model and map to the limits of the resolution of the crystal (which is limited by the level of order or disorder in the crystal). The crystallographer then deposits a model of the asymmetric unit of the crystal in the PDB, along with the experimental diffraction data (amplitudes and widths of the X-ray reflection spots, or "structure factors") from which the electron density map can be reconstructed.
Examining the correspondence between the model and the electron density map (EDM) provides much clearer insight into the uncertainties in the model than does merely examining the model itself (see also
<a href="http://proteopedia.org/wiki/index.php/Quality_assessment_for_molecular_models" target="_blank">
Quality assessment for molecular models</a>). Crystallographers generally use heavy duty
visualization and modeling software such as
<a href="http://proteopedia.org/wiki/index.php/Molecular_modeling_and_visualization_software" target="_blank">
Coot</a>
or
<a href="http://proteopedia.org/wiki/index.php/PyMOL" target="_blank">
PyMOL</a>, which require considerable practice to use effectively.
<a href="http://jmol.org" target="_blank">
Jmol</a>
first became capable of displaying electron density maps in January, 2010. Being able to display EDM's in Jmol opens the door to examining EDMs effectively in a web browser, with a user interface (yet to be developed) that requires no specialized software knowledge. Until such an interface becomes available,
the methods demonstrated here can be utilized.
See AlsoSee Also
Please see X-ray crystallography and Resolution, which include images of electron density maps.