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Cursus: SK-B2RDEM
SK-B2RDEM
Rontgendiffractie en electronenmicroscoop
Cursus informatie
CursuscodeSK-B2RDEM
Studiepunten (EC)7,5
Cursusdoelen
After completing the course the students are capable of:
1 Understanding the interaction of electromagnetic radiation with matter
1 Understanding periodic arrangement of molecules/atoms in crystals
1 Understanding symmetry and Bravais lattices
1 Understand crystal and reciprocal coordinate systems
1 understanding the basics of (cryo) electron microscopy and (cryo) specimen preparation
1 basic technical understanding of TEM microscopes
1 Understand the basics of cryo single particle data acquisition and data analysis
 
2 Draw net planes in a crystal lattice
2 Calculating d-spacings of net-plane series: use the correct formula for the crystal system
2 Using Bragg’s law to solve structure from powder data
2 Understanding Data collection strategies and Ewald sphere
2 Understand the principle of 3D  reconstruction from projection images
2 Concept of image classification
 
3 Applying symmetry operations on atoms
3 Calculate structures factor from atomic positions
3 Understanding resolution
3 Understanding the phase problem
3 Using the Patterson method
3 Phasing from anomalous data
3 Understanding unit cells content, packing, disorder and solvent channels
3 Electron densities from Fourier summation
3 Refining protein structures
3 Determine resolution in (cryo)EM reconstructions
3 Reconstruction of object from projections
3 Apply basic image processing operations
 
4 Reading crystallographic papers
4 Structure validation
4 Reading EM papers
 
5 Use crystal structure for answering chemical research questions
5 Use crystal structure for answering biological research questions
5 Choose a suitable  EM technique for answering biological research questions.
Inhoud
For the understanding of materials properties, the working of chemical substances or complex macromolecular machines, the knowledge of the 3D structure is indispensable. In this course you will learn the fundamentals of scattering, diffraction and imaging techniques.
Crystalline materials consist of ordered arrays of molecules that can diffract X-rays in well-defined directions. The directions and intensities of the scattered beams allows us to unravel the underlying structure. Properties of the materials can be understood and new materials can be designed. An important application of crystal structure analysis is the determination of the molecular structures of organic compounds and proteins at high resolution, higher  than possible with any other technique.
Electron microscopy allows imaging of small objects, ranging from whole cells to single molecules.Cryo-EM techniques and image reconstruction algorithms allow high resolution structure determination of single molecules in vitro and in situ.
  
Course content:
Crystals: three dimensional long range order, lattices and symmetry
Scattering: interaction of electromagnetic waves and electrons with matter, wave theory, phase differences and complex numbers, resolution
Diffraction: reciprocal space, diffracted intensity, Fourier synthesis and analysis
Phasing: phase problem and electron densities
Structure determination: refinement and validation
Fundamental principles of TEM
Instrumentation, detectors ,lenses, phase plate, back focal plane
Cryo EM: sample preparation, imaging, resolution, phase contrast
3D EM: single particle analysis, electron tomography, helical reconstruction
 
Course material Home assigment/Computer practice
Reader: X-ray Crystallography
Crystals: periodic lattices and symmetry
Bragg’s law
Reciprocal space: indexing
Diffracted intensities
 
 
 
 
Home assignment: Solving cubic inorganic structure from powder pattern
 
Fourier theory
Phase problem
Structural calculations
Computer practice: Solving small molecule structure with Patterson method
 
 
 
 
Reader:  Protein Crystallography
Crystallization
Data collection:  Beam lines and Ewald construction
Data processing
 
 
Compter practice: Process  protein crystal diffraction data
Phasing
Refinement
Validation
Computer practice: Phasing from anomalous data, calculate electron density, refine structure, validate protein molecular structure
Reader: Electronmicroscopy
3D TEM
Cryo Spec preparation
Cryo Data acquisition
Data analysis Cellular
Data analysis Single Particle
 
 
 
Computer practice: Image processing, MATLAB
 
Home assignment: EM paper
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