Henderson-Hasselbalch equation = where it comes from & when and how to use it @thebumblingbiochemist

Updated September 2026, 3 weeks ago

Henderson-Hasselbalch equation = where it comes from & when and how to use it

$Assemblies, asymmetric units, models & unit cells oh my! Different PDB views of crystal structures A crystal is made up of lots and lots and lots of copies of the molecule(s) you’re trying to look at arranged in a repeating 3D pattern. Each copy is too tiny to see by itself, but if you put a ton of them together, their signals can contribute to each other such that you get a strong enough spots on the diffraction pattern to work back from. That protein or complex you’re interested is looking at is usually the “biological assembly” which is the form of the molecule that is thought to be the active form. But, if you look at the “Model” in the 3D viewer, you might see something different. This is because it’s showing you the “asymmetric unit” which is the smallest repeating part of the crystal. If you know the structure of the asymmetric unit and the dimensions of something called the unit cell, you can recreate the whole crystal just using symmetry operations (rotate, move left, move up, etc.). Confusingly, that asymmetric unit might itself contain more than one copy of the biological assembly. The copies of the biological assembly within the asymmetric unit are identical in their sequence but they might be slightly different in their shape, and during the structure-solving they are therefore treated separately. In the PDB, these “different copies” within the asymmetric unit are called “instances” so if you’re confused by that, that’s what it refers to and you can choose which one you want to look at. In sum: * Crystal lattice: the “whole” crystal - it contains lots and lots (billions typically!) of copies of the thing you care about * Unit cell: the basic repeating unit of a crystal, like the bricks in a brick wall * Asymmetric unit: The smallest “unique” part of the crystal * Biological assembly: The biologically relevant form - might be different than the asymmetric unit. Each unit cell has one or more full or partial copies of the asymmetric unit Copies of the asymmetric unit are related to one another symmetrically through space group transformations to build up the unit cell. Unit cells are positionally related through lattice transformations to build the entire crystal. much more here: http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies 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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$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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