Your LB/agar plate has colonies. Yay! Now what? @thebumblingbiochemist

Updated September 2026, 2 weeks ago

Your LB/agar plate has colonies. Yay! Now what?

$Interpreting Table 1 crystallography data Even when it’s not actually “Table 1,” crystallographers often use the term “Table 1” to refer to the table of statistics used to report the quality of their structural model and the underlying data, as well as some of the parameters about how the data was collected and processed. For more . . . evaluating structural quality: https://thebumblingbiochemist.com/365-days-of-science/structurequality/ more on crystallography: http://bit.ly/xraycrystallography2 The video gets pretty deep, and if you want to go even deeper…. Fu, Z.-Q.; Geisbrecht, B. V.; Bouyain, S.; Dyda, F.; Chrzas, J.; Kandavelu, P.; Miller, D. J.; Wang, B.-C. I/σI vs {Rmerg, Rmeas, Rpim, CC1/2} for Crystal Diffraction Data Quality Evaluation. bioRxiv February 2, 2025, p 2024.12.10.627855. https://doi.org/10.1101/2024.12.10.627855. Read, R. J.; Adams, P. D.; Arendall, W. B.; Brunger, A. T.; Emsley, P.; Joosten, R. P.; Kleywegt, G. J.; Krissinel, E. B.; Lütteke, T.; Otwinowski, Z.; Perrakis, A.; Richardson, J. S.; Sheffler, W. H.; Smith, J. L.; Tickle, I. J.; Vriend, G.; Zwart, P. H. A New Generation of Crystallographic Validation Tools for the Protein Data Bank. Structure 2011, 19 (10), 1395–1412. https://doi.org/10.1016/j.str.2011.08.006. Shabalin, I. G.; Porebski, P. J.; Minor, W. Refining the Macromolecular Model - Achieving the Best Agreement with the Data from X-Ray Diffraction Experiment. Crystallogr Rev 2018, 24 (4), 236–262. https://doi.org/10.1080/0889311X.2018.1521805. Lamb, A. L.; Kappock, T. J.; Silvaggi, N. R. You Are Lost without a Map: Navigating the Sea of Protein Structures. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2015, 1854 (4), 258–268. https://doi.org/10.1016/j.bbapap.2014.12.021. Wlodawer, A.; Minor, W.; Dauter, Z.; Jaskolski, M. Protein Crystallography for Aspiring Crystallographers or How to Avoid Pitfalls and Traps in Macromolecular Structure Determination. The FEBS Journal 2013, 280 (22), 5705–5736. https://doi.org/10.1111/febs.12495. McPherson, A.; Gavira, J. A. Introduction to Protein Crystallization. Acta Crystallographica Section F:Structural Biology Communications 2014, 70 (1), 2–20. https://doi.org/10.1107/S2053230X13033141. Wlodawer, A.; Minor, W.; Dauter, Z.; Jaskolski, M. Protein Crystallography for Non-Crystallographers, or How to Get the Best (but Not More) from Published Macromolecular Structures. FEBS Journal 2008, 275 (1), 1–21. https://doi.org/10.1111/j.1742-4658.2007.06178.x. Smyth, M. S.; Martin, J. H. X Ray Crystallography. Journal of Clinical Pathology: Molecular Pathology 2000, 53 (1), 8–14. https://doi.org/10.1136/mp.53.1.8. And here’s the paper whose Table 1 I used: Flydal, M. I.; Alcorlo-Pagés, M.; Johannessen, F. G.; Martínez-Caballero, S.; Skjærven, L.; Fernandez-Leiro, R.; Martinez, A.; Hermoso, J. A. Structure of Full-Length Human Phenylalanine Hydroxylase in Complex with Tetrahydrobiopterin. Proceedings of the National Academy of Sciences 2019, 116 (23), 11229–11234. https://doi.org/10.1073/pnas.1902639116. more on PDB entries: https://bit.ly/pdbstructures Structural biology resources guide: https://bit.ly/structural_biology My structural biology YouTube playlist: https://youtube.com/playlist?list=PLUWsCDtjESrGhwVxsRbTJdL-BEsN60RCs My x-ray crystallography YouTube playlist: https://www.youtube.com/playlist?list=PLUWsCDtjESrHIGzgUctYRWSWm-lw9_VhX more on crystallography here: http://bit.ly/xraycrystallography2 more about all sorts of things: #365DaysOfScience All (with topics listed) 👉 http://bit.ly/2OllAB0 or search blog: http://thebumblingbiochemist.com ⠀ #scicomm #biochemistry #molecularbiology #biology #sciencelife #science #realtimechem$

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