X-ray crystallography maps (viewing & understanding 2Fo-Fc, Fo-Fc, etc.) & overview of phase problem

[@thebumblingbiochemist]

Lamb, A. L., Kappock, T. J., & Silvaggi, N. R. (2015). You are lost without a map: Navigating the sea of protein structures. Biochimica et biophysica acta, 1854(4), 258-268. doi.org/10.1016/j.bbapap.2014.12.02
Introduction to Macromolecular Crystallography, Second Edition, Alexander McPherson 
First published:11 March 2008.Print ISBN:9780470185902 |Online ISBN:9780470391518 |DOI:10.1002/9780470391518  
 
I had the pleasure of sitting in on the CSHL crystallography course twice and learning directly from Dr. McPherson (and a who’s who list of great crystallographers!). This book is really good and explains things in a comprehensive way that’s still comprehendible! It doesn’t get too into the math and instead helps you get a more intuitive sense of what’s going on. Highly recommend. 
 
Crystallography Made Crystal Clear: A Guide for Users of Macromolecular Models, Gale Rhodes. ISBN 0080455549, 9780080455549 books.google.com/books/about/Crystallography_Made_Crystal_Clear.html?id=rwnR6qvaWgkC&source=kp_book_description  
 
This is a more “meaty” book for those interested in really getting it down.  
 
Articles: 
“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. febs.onlinelibrary.wiley.com/doi/full/10.1111/j.1742-4658.2007.06178.x  
 
This is probably one of my most-reread articles. It does a great job explaining the basics of how to go about critically interpreting the quality of protein crystal structures, what to keep an eye out for, and what the basic statistics mean. 
 
Websites:  
 
Resources for Readers of Crystallography Made Crystal Clear 
spdbv.vital-it.ch/TheMolecularLevel/CMCC/index.html  
 
This goes along with that book, but you don’t need the book to appreciate it. It has links to TONS of useful software programs and articles for learning about crystallography 
 
Protein Crystallography Course, Randy Read. Clear visuals & explanations. www-structmed.cimr.cam.ac.uk/course.html  
 
Lectures: 
  
If you want to get hard-core into the nitty gritty of protein crystallography, Dr. Andrea Thorn has a great TH-cam series of videos, “Basics of Macromolecular Crystallography”: th-cam.com/play/PLHHBmgJ8vFm6xZPlWlRGuBaoOM3OGlN5T.html   
More about PyMol: more about PyMol: bit.ly/pymolintro  
more on resolution: blog: bit.ly/structure_resolution ; TH-cam: th-cam.com/video/Ijm-nDzLWhA/w-d-xo.html   th-cam.com/video/1DZClUKowsY/w-d-xo.html
   
and this intro video: TH-cam: th-cam.com/video/t5WeMkY0skU/w-d-xo.html    
  
more on understanding crystal structures: bit.ly/crystalstructuremodels & th-cam.com/video/YK3VkqD2o2s/w-d-xo.html   
   
intro to PDB, crystal structure entries, crystal contents, resolution: bit.ly/pdbstructures & th-cam.com/video/Re2gwi-_OEw/w-d-xo.html & th-cam.com/video/IZtHsUFbyes/w-d-xo.html     
   
links to more about the GFP example structure:   
   
www.rcsb.org/structure/2b3p    
   
Pédelacq, J. D., Cabantous, S., Tran, T., Terwilliger, T. C., & Waldo, G. S. (2006). Engineering and characterization of a superfolder green fluorescent protein. Nature biotechnology, 24(1), 79-88. doi.org/10.1038/nbt1172    
   
pdb101.rcsb.org/motm/42    
 
more about all sorts of things: #365DaysOfScience All (with topics listed) 👉 bit.ly/2OllAB0 or search blog: thebumblingbiochemist.com

[@spaceraccoonx]

Amazing video. Didnt understand it at all beforehand. Thanks🙏

[@thebumblingbiochemist]

Glad it helped!

[@noahpieta8888]

Really brief and clear explanation! Really appreciate 👍

[@thebumblingbiochemist]

So relieved to hear! It's always tricky to try to explain these technical and nuanced aspects! Really glad I could help