By taking X-rays of the protein from multiple angles, we can construct a digital 3D model (called an electron density map
) with the rough outlines of the protein's actual shape.
Resolution in terms of electron density is a measure of the resolvability in the electron density map
of a molecule.
This is because the crystal structure is solved using the electron density map
, and the electrons of the hydrogen atom are mostly between the hydrogen and carbon atoms' nuclei in the sigma bond.
The final step in protein crystallography is model building, or determining coordinates of atoms from an electron density map
. Model building is typically a two-stage process.
The software program carries out all the steps of macromolecular structure determination from scaling data to calculation of an electron density map
By changing the orientation of the crystal, and then measuring and analyzing the angles and intensities of the beams, also known as reflections, the structure of the protein can be modeled using computers to create an electron density map
and three-dimensional model.
By comparing the resulting patterns of scattered X-rays for the two crystal variants, the researchers were able to "back-calculate' an electron density map
that effectively shows the atomic structure of the molecule with a resolution of 3.5 angstroms or ten-billionths of a meter.
The electron density maps
are then interpreted using methods that dock and refine atomic or homology models or by building de novo atomic models [21-23].
She begins with the fundamentals such as unit cell calculation, point groups reciprocal lattice, properties of X-rays, and electron density maps
. Then she illustrates seven specific crystal systems with examples, among them a monocline system with sucrose, an orthorhombic system with polyethylene, a hexagonal system with magnesium, and a cubic system with acetylene.
Some specific areas explored include proton charge transport in nafion nanochannels, optical properties of non-periodic dielectric systems made of nanostructured porous silicon, Fourier electron density maps
for nanostructured sol-gel solids, and the effects of morphology on the electronic properties of hydrogenated silicon carbide nanowires.
Examination of the electron density maps
revealed that the protein is not SP17.