The Structural Biology Resource Page
This page provides links to structural biology resources into four areas, cryo-electron microscopy, crystallization, X-ray data collection, and other resources. The first three cover research services offered at the Hauptman-Woodward Medical Research Institute through Our Cryo-EM Center, Crystallization Center and the staff of the IMCA-CAT beamline at the Advanced Photon Source.
We highly recommend joining the American Crystallographic Association housed in our Institute. They support interests in all four of the resource areas that this page covers.
Cryo-EM resources include key papers, books, articles, online resources, videos, cryo-EM centers, and workshops to introduce the technique. Our Cryo-EM Center provides sample preparation, characterization, full data collection, and analysis of single-particle samples. Click on the icons to the right of the categories to see details.
Papers, books, and articles providing practical advice
- Specimen preparation for high-resolution cryo-EM.
- Sample preparation of biological macromolecular assemblies for the determination of high-resolution structures by cryo-electron microscopy.
- Cryo-EM grid preparation of membrane protein samples for single particle analysis.
- A primer to single-particle cryo-electron microscopy.
- High-resolution cryo-EM: the nuts and bolts.
Useful online resources
Crystallization resources include key papers, books, articles, online resources, vendors, crystallization centers, videos, and meetings and workshops. Our Crystallization Screening Center has been operating for over two decades following the principals of many of these resources and provides a rapid and efficient crystallization service to quickly assess if a project is amenable to a crystallographic approach. Provide a protein sample and we do the rest. Details on how to accomplish this are given on the Center’s page. Below are a set of resources that explain the basic to advanced concepts to crystallization, vendors, other Centers like ours across the world, and other useful information. Click the icon on the right to see the list.
Papers, books, and articles providing practical advice
Acta Crystallographica Section F, Structural Biology Communications produced a virtual issue entitled “Protein Crystallization – state of the art” with a series of papers covering many aspects of crystallization. We highly recommend the series and have highlighted ones that may be of particular interest for those thinking of exploring the field with *.
- Introduction to protein crystallization*
- Approaches to automated protein crystal harvesting
- Nucleation precursors in protein crystallization
- Mechanisms, kinetics, impurities and defects: consequences in macromolecular crystallization
- Applications of the second virial coefficient: protein crystallization and solubility
- Automation in protein crystallization
- Crystallization screening: the influence of history on current practice* (From our own Crystallization Center – how different crystallization screens have developed and the thinking behind them)
- Identifying, studying and making good use of macromolecular crystals* (From our own Crystallization Center)
- Microseed matrix screening for optimization in protein crystallization: what have we learned?*
- A drunken search in crystallization space*
- Optimization of crystallization conditions for biological macromolecules*
- Membrane proteins, detergents and crystals: what is the state of the art?*
- A comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes*
- Latest methods of fluorescence-based protein crystal identification
- Origin and use of crystallization phase diagrams*
- Large-volume protein crystal growth for neutron macromolecular crystallography
- Practical macromolecular cryocrystallography*
- In vivo protein crystallization in combination with highly brilliant radiation sources offers novel opportunities for the structural analysis of post-translationally modified eukaryotic proteins
- The role of mass transport in protein crystallization
There are a number of good books on the subject and we list a few which we regard as essential in the laboratory.
- Biomolecular Crystallography: Principles, Practice, and Application to Structural Biology by Bernhard Rupp – A comprehensive guide to crystallographic practices in general.
- Protein Crystallization, Second Edition (IUL Biotechnology Series) 2nd Edition by Terese Bergfors
- Crystallization of Biological Macromolecules by Alexander McPherson
Other papers that are recommended include:
- The protein as the variable in protein crystallization (the protein can be the most significant variable and molecular biology approaches can be an efficient means to promote successful crystallization)
- Membrane Protein Crystallization.
- What’s in a drop? Correlating observations and outcomes to guide macromolecular crystallization experiments (the paper discusses the interpretation of crystallization screening results in the context of a comprehensive picture of all the outcomes rather than focusing on crystal or no crystal).
- Lessons from high-throughput protein crystallization screening: 10 years of practical experience. (an explanation of the development of the screens and processed used in our own Crystallization Center).
- A review of techniques for maximizing diffraction from a protein crystal in stilla (a review of crystallization and sample preparation techniques to enhance the resulting data quality).
- An overview of biological macromolecule crystallization.
Other material that may be useful.
- Mitegen have information on crystal mounting and have a range of posters for the lab describing crystallization plate tips, harvesting, and cryoprotecting.
- Hampton Research have assembled a comprehensive set of guides on the hard-learned empirical basics of crystallization entitled crystallization 101. These are highly recommended.
Useful online resources
- Comparison of crystallization conditions – Compares similarity between different commercial and custom designed crystallization screens
- Biological Macromolecule Crystal Database
- Isoelectric point calculator
- Crystallization predictor – FDETECT
- Prediction of crystallization probability based on pI
- XtalPred prediction of crystallization
- pH calculator for crystallization cocktails
- Hampton Research provide an extensive range of crystallization supplies.
- Mitegen provide a range of consumables and specialize in crystal growth, mounting, and cryo-EM products
- Molecular dimensions also provide an extensive range of crystallization supplies.
- Formulatrix provide crystallization instrumentation used by the Crystallization Screening Center
- sptlabtech provide crystallization instrumentation
- Art Robbins Instruments provide crystallization instruments
Meetings and workshops
With the COVID-19 pandemic many meetings are delayed, especially when they contain practical aspects associated with crystallization.
- X-ray Methods in Structural Biology at Cold Spring Harbor. An intense crystallography course with crystallization included.
- Advanced Methods in Crystallization course in Move Harde, Czech Republic
- International School on Biological Crystallization, Granada Spain.
- From Proteins to Crystals (a top level guide to taking a protein to a crystal – suitable for those with an interest in science but no expertise required).
- Protein crystallization (a simple guide to basic crystallization setup – an advanced tip is to use a wine cork to stamp grease over the wells)
- Hanging drop vapor diffusion crystallization tutorial (the basic technique used by most people starting crystallization)
- Protein crystallization hanging drop vapor diffusion (another take on the same technique)
- Crystallization of membrane proteins in lipidic cubic phases (a successful approach used to crystallize membrane proteins)
- Protein Crystals – Backstage Science (a nice video that shows a little of what goes on in a crystallographic project)
- Basics of Macromolecular Crystallography (a longer but very detailed survey of crystallization techniques)
- Lysozyme crystal growth (watch crystals grow speeded up quite a bit from a protein extracted from chicken eggs)
High-throughput Crystallization Centers worldwide
X-ray Data Collection Resources
X-ray data collection resources include useful reading material, sample preparation guides, data collection and processing software, laboratory X-ray systems, synchrotron beamlines, and meetings and workshops. We recommend the Industrial Macromolecular Crystallography Association – Collaborative Access Team beamline, a facility we run for industry at the Advanced Photon Source that supports proprietary studies but which is also available for non-proprietary research and brings the experience of operations for six of the top ten pharmaceutical companies to all.
Below is a selection of resources to help the process once you get a crystal. Useful reading matter is listed followed by sample preparation guidelines, resources on data processing, and also information about laboratory X-ray systems. We also list beamlines throughout the US and recommended meetings to learn more.
- Demystifying the synchrotron trip: a first time user’s guide.
- Carrying out an optimal experiment.
- Macromolecular crystallography with synchrotron radiation. A comprehensive and detailed guide for those that want to understand synchrotron potentials fully.
Sample preparation guidelines
- Sample preparation and mass-spectrometric characterization of crystal-derived protein samples (a useful step to confirm that the crystal you have is what you think it is and if there have been any modifications during the crystallization process)
- Macromolecular cryocrystallography – methods for cooling and mounting crystals at cryogenic temperatures (practical guidance to prepare cryocooled crystals for study)
- Cryocooling and radiation damage in macromolecular crystallography (practical techniques for successfully cryocooling crystal with a background on the theory behind the practice).
Data collection and processing software
Meetings and workshops
With the COVID-19 pandemic, many meetings are delayed, especially when they contain practical aspects associated with crystallization.
Complementary structural biology techniques
Small Angle X-ray Scattering.
- Small Angle X-Ray and Neutron Scattering from Solutions of Biological Macromolecules, Svergun, Koch, Timmins & May
- Biological Small Angle Scattering: Theory and Practice, Lattman, Grant & Snell
- Biological Small Angle Scattering: Techniques, Strategies and Tips (Advances in Experimental Medicine and Biology) Chaudhuri, Munoz, Qian & Urban
- Beamline 4-2, Small-angle X-ray scattering/diffraction at SSRL
- Beamline 18-ID, BIOCAT SAXS/WAXS of biological solutions at the APS
- Beamline 14-ID, BioCARS Time-resolved SAXS at the APS
- Beamline 16-ID, Life Science X-ray Scattering (LiX) NSLS II
- Beamline 12.3.1, the SIBYLS beamline at the ALS
- Beamline 7A, BioSAXS at CHESS