Crystallography Skills

Learning x-ray crystallography has been fascinating so far. Contrasting many other projects, my work does not require a wealth of research before beginning to learn and apply certain skills. I have spent the last four weeks honing my crystallography skills, and reading about theory in my spare time. This post will mostly cover the day to day challenges I’ve faced.

When I first arrived to campus, the x-ray diffractometer (XRD) was undergoing some minor repairs due to cooling issues.  The XRD is a precise piece of equipment that basically fills up its own small room. In the space around the XRD, we have just enough room for numerous temperature control/air conditioning systems that must all be working for the machine to run. There is a roughing chiller that brings the sample down to about -5°C, then a cryostream jet of nitrogen takes the sample’s temperature down to -173°C. The cryostream needs liquid nitrogen from a large dewar, but it also must have a dry air blower. If the jet of air has any moisture, it will cover the sample in frost, or turn the inside of the XRD into a giant snow globe. The roughing chiller uses water pumps which needed replaced before any experiments could be run. This was a standard plumbing problem that required some elbow grease, towels, and new tubing. Fortunately, this problem only took a few days to fix.

Samples are chilled to -173°C (-279°F), for a couple reasons: first, warm crystals have greater thermal vibrations that could decrease the resolution of harvested x-ray reflections, and secondly, low temperatures mean less solvent loss. I learned the hard way that this can destroy crystal samples. The skill that seemed the most daunting at first, though I have grown to enjoy it, is mounting crystals. Samples either come from labs in the ISC or from collaborators at different colleges. Crystallographers should be able to handle parsing the given sample for a crystal that is not too big or too small, then gluing it to the end of a glass fiber. The glass fiber is embedded in a brass cap, which is placed in a goniometer, so that it can be centered in the XRD. The crystals are usually 0.25 mm or less in any dimension, so mounting them requires a microscope, a steady hand, and an enormous amount of patience. I learned that many of the simple steps in solving structures help along the next step. For example, if a crystal is shaped like a needle, it may seem easier to put it on the end of the fiber such that it makes a T-shape. However, standing the crystal on its end will make centering the crystal and indexing crystal faces exceptionally easier.

Other than becoming accustomed with mounting crystals, I also needed to learn the ways to use the different software that allows for processing and analyzing data. APEX3 is the software that takes hundreds of collected x-ray reflections and turns them into an initial structure solution. It also helps us determine which crystal samples are the most orderly or bright. Before running a full experiment with hundreds of frames, we run unit cells (also called matrix scans). These matrix scans allow us a peek into the structure before committing hours to running a full experiment. Below, in red, is a picture of a frame from the middle of an experiment. The yellow spots represent measured reflections where x-rays diffracted off electron density in the crystal sample. These spots are harvested and integrated across all frames in the experiment to give an initial structure with a certain space group. I will talk more about space groups and interpreting results in my next post.

The spots are reflections of x-rays that diffracted off of electron clouds.

This view lets me qualitatively and quantitatively determine the resolution of the spots. Some crystal samples need replaced when running unit cells because their reflections are too weak or because the crystal is twinned.


This shows a very orderly crystal sent from a collaborator.

This shows a very orderly crystal sent from a collaborator.

The dots on the blue background represent the reciprocal lattice viewer. Looking along any of the cells axes should show dots in equally spaced rows. If the dots appear jumbled up or with dots almost overlapping in slightly shifted rows then the crystal is twinned. Twinning occurs when a new crystal starts growing right next to another one. This causes the x-rays to diffract off two different lattices. The program struggles to solve structures with lattices that are offset, so it is my job as the crystallographer to find the sample that will give us the most accurate initial solution.