Why we use X-rays to visualize protein molecules.

In order to visualize a very small object, such as a cell, one magnifies the object using a light microscope. When using a light microscope, light bounces off the object and the scattered light’s intensity and phase are reassembled and magnified by the objective lens (Fig. 1 is a diagram of a light microscope). However, the light microscope can only be used to visualize objects no smaller than the wavelength of light being used which is ~500 nanometers (nm). Therefore, in order to visualize individual atoms within a protein molecule, X-rays are the correct light source as their wavelength of ~0.1 nm matches the typical distance between two atoms within a protein molecule. Unfortunately, while X-rays are the correct wavelength, their diffracted intensity and phase are unable to be reassembled by an objective lense as X-rays pass right through most material. Therefore, we must substitute the objective lense with X-ray crystallography. Here we can directly measure the diffracted intensity of each reflection but must indirectly extrapolate each reflections phase. This phase and intensity information is used in a mathematical calculation, known as the Fourier Transformation, to generate an electron density map of the protein molecule that can be readily visualized on a molecular graphics terminal and used to build a molecular model of the protein.