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X-ray crystallography helps us understand chemistry and biology
Life takes place in 3D. That is true both in our every-day life and at the molecular level. To understand how a machine or device is working, like a clock or an engine, we can look at how its different parts are put together. The same goes for molecules – if we know their 3D-shape, we can understand why they work as they do. For example – how does the protein that detects light in our eyes work, or why does a drug have a certain effect?
Unfortunately, molecules are much too small to be observed even in the most powerful of microscopes. Therefore, we have to use other methods to find out what they look like. One very good method is X-ray crystallography. For this, you need a crystal of the molecule you are interested in and X-rays. When you shoot at a crystal with X-rays, the rays will be spread in a regular pattern, creating spots on the detector that is placed behind the crystal. If you analyze this pattern, where the dots are and their intensity, it is possible to create a model of how the molecules that create this pattern must look like.
What is a crystal?
A crystal is something extremely ordered. One example is ordinary table salt, sodium chloride. If you look closely at the table salt at home, you will see that it actually consists of small cube shaped crystals. In a sodium chloride crystal, the sodium and chloride atoms are sitting next to each other in a very defined, repeating pattern. The 3D shape, or structure, of sodium chloride was the first one to be determined in 1912. Since then, scientists have developed the technique to study crystals of larger and more complex molecules, like the molecules that build up our bodies and perform the many tasks that we take for granted – like seeing, digesting food, or transport oxygen to all our cells. How do they perform their tasks, and when they fail and someone get a disease, how can this be explained? X-ray crystallographers have played a huge role in shedding light on questions like these. Several of them have received the Noble Prize for their discoveries. Nevertheless, many riddles remain to be solved!
Ok. What do you need to perform an X-ray diffraction experiment and determine the structure of a molecule? Well, a machine that creates X-rays, a high quality crystal, and a detector that records the diffraction.
How are the X-rays created?
X-rays are electromagnetic radiation – just like visible light, but with much shorter wavelength. It is important that the wavelength of the rays is of similar magnitude as the details you want to study in your molecule. This usually means around 1 Ångström; a tenth of a billionth of a meter. Molecules certainly are tiny!
The X-rays that are used for an experiment need to be of very high quality. You can often use a smaller machine that you can have at home in your laboratory, but if you work with more sensitive material like many biological molecules, you need to use X-ray radiation from a synchrotron. A synchrotron is a type of particle accelerator where electrons emit X-rays when they are circling near the speed of light in a large orbit, several hundred meters in diameter. These huge research facilities exist at a few places around the world, and scientists travel to them to test their precious samples.
What happens when the X-rays hit the crystal?
The spreading of X-rays by crystals is called diffraction. The X-rays are electromagnetic radiation, just like ordinary light, but with much shorter wavelength. When the X-rays hit the electrons in the molecules in the crystal they bounce off in various directions. At certain angles, they reinforce each other. At these positions, a spot is created on the detector. The crystal is rotated so that every angle of it is illuminated and diffraction is recorded.
Creating the picture of the molecule
Once all the data is collected, the position and intensity of the spots are analyzed. Several other parameters also need to be determined. The most important and difficult of these is the phase of the X-ray that created the spot. Once all of this is established, the data extracted from the spots can be transformed into electron density. The electron density shows where there are a lot of electrons in the molecule – that is, where there are atoms. Then you can build a model of the molecule you are investigating into the electron density, and begin to evaluate on how it works! The resolution determines the amount of details you can see. That is: how close can two spots be and still be separated. In the case of X-ray diffraction, the resolution depends both on the quality of the crystal and the quality of the X-rays. It is comparable to a photo – the better the resolution of the camera, and the more still the motive is, the more detail you can see. In X-ray crystallography, this means understanding more chemistry and biology.
Most popular video
A (not so serious) introduction to an X-ray diffractometer
How can we determine the structure of large molecules? Some young scientists show the instrument they use to do X-ray crystallography, in a very relaxed way...
Article by Anna Frick, University of Gothenburg, Sweden