X-ray crystallography is a technique where we look at protein (or other molecules’) atomic structures (where the different individual carbons, nitrogens, oxygens, etc. are) by beaming x-rays at crystals of those molecules. The x-rays gets scattered from the atoms’ electrons and the scattered rays interact, combining together in certain situations to give strong waves. We can then capture those “diffracted” x-rays on a detector and work backwards from the pattern of spots (diffraction pattern) to find the positions of the electrons that caused the scattering. And then we can build an atomic model into that electron density map. And then do a lot of iterative refinement trying to get the model and map to fit. In this video, I go over the basics of x-ray crystallography models & maps, and what you’re actually admiring when you “get lost” in a good structure in a PyMol or Coot… Some theory and practical info towards the end on how you can play around for yourself. If you want to know more about x-ray crystallography, see: http://bit.ly/xraycrystallography2
for more on understanding and interpreting resolution: https://bit.ly/structure_resolution
link to video: https://youtu.be/YK3VkqD2o2s
If you want to know more about x-ray crystallography, see: http://bit.ly/xraycrystallography2
more about the PDB & structures: https://bit.ly/pdbstructures ; video: https://youtu.be/NgXwP7gGPyA
more about PyMol: https://bit.ly/pymolintro & https://bit.ly/pymolmovies
and, more importantly, there’s a lot of great resources at RCSB PDB 101: http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data
If you’re interested in learning more about how to evaluate the quality of published structures for yourself, I highly recommend the free article, “Protein crystallography for non‐crystallographers, or how to get the best (but not more) from published macromolecular structures” by Alexander Wlodawer, Wladek Minor, Zbigniew Dauter, and Mariusz Jaskolski. It is literally one of my all-time favorites. They do a really great job explaining what the various terms mean, what to look out for, etc. https://febs.onlinelibrary.wiley.com/doi/full/10.1111/j.1742-4658.2007.06178.x
And if you want to get hard-core into the nitty gritty of protein crystallography, Dr. Andrea Thorn has a great YouTube series of videos, “Basics of Macromolecular Crystallography”: https://youtube.com/playlist?list=PLHHBmgJ8vFm6xZPlWlRGuBaoOM3OGlN5T
I also have some more posts & YouTube videos on various aspects of what “doing crystallography” looks like: https://youtube.com/playlist?list=PLUWsCDtjESrHIGzgUctYRWSWm-lw9_VhX
