Applied Cryo-Electron Microscopy

Course goals

At the end of the course, you should be able to:
 

• Describe important hardware components of the electron microscope, and relate the hardware to the expected data quality
• Understand sample preparation requirements and strategies for single particle analysis and tomography
• Evaluate raw data quality using established metrics
• Perform tomographic and single particle reconstructions from raw data

Critically assess published cryo-EM structures
 

Toetsvorm	Omschrijving	Weging
Practicals	Demonstrate ability to do critically assess and process data	20
Presentation	Presentation of cryo-EM literature to fellow students and teachers	30
Test	Written test covering course content	50

Content

Description of content Cryo-electron microscopy (cryo-EM) is a structural biology technique used to investigate biomolecular (protein) complexes both within their native cellular context and at near atomic resolution when purified. In this course we will cover the fundamental aspects of sample preparation, image acquisition and data processing. By the end of the course students should understand how cryo-EM can address research questions related to structural biology while appreciating its limitations and the required time investments. This course will focus on the practical aspects of doing cryo-EM within a research setting. The necessary hardware components and how they relate to data quality will be discussed and demonstrated during laboratory practicals. Sample preparation methods for high quality data acquisition will be explained, as well as solutions to common preparation challenges that limit the accessible information. The underlying physics and mathematics to describe image formation will be treated in a mostly qualitative manner with enough depth to understand standard data processing methods. Students will process raw data during computer practicals to explore single particle and tomographic reconstructions. Common metrics used to evaluate both the quality of the raw data and the quality of the resulting reconstruction(s) will be discussed. Students will also present recent publications of cryo-EM structures or methods. This will put into practice critically assessing deposited electron density maps and (if available) the corresponding atomic model(s), as well as further the appreciation of hardware/software developments. This course is aimed at students who intend to solve structures themselves using cryo-EM and those who wish to use the information that protein structure databases provide in a critical manner. The course will meet one day a week for a mixture of lectures, tutorials, practicals or presentations. Literature/study material used: Reader assembled from Williams, D. B. and C. B. Carter (2009). Transmission electron microscopy : a textbook for materials science. New York, Springer. Mandatory for students in Master’s programme: No. Optional for students in other Master’s programmes GS-LS: YES