3 ECTS credits
75 h study time
Offer 1 with catalog number 4006472FNR for all students in the 1st semester of even academic years (e.g. 2012-2013) at a (F) Master - specialised level.
This class deals with a detailed study of structural analysis of macromolecules (and proteins in particular) using X-ray crystallography. The course starts with an overview of the basic principles (reciprocal space, sphere of Ewald, structure factor, Laue conditions). This is followed by a discussion of crystal symmetry in real space (point groups, space roups, crystal lattices) and in reciprocal space. The different X-rays sources and detectors are introduced and the strategies used to grow crystals and collect diffraction data are discussed. The Phase problem and the Patterson function are introduced, followed by an in depth presentation of the techniques used for phase determination: isomorphous replacement, anomalous scatter and molecular replacement. The next chapter deals with techniques used to improve initial phases: solvent flattening, histogram matching, NCS averaging, direct methods, ... . This is followed by model building techniques with emphasis on automated methods for secondary structure recognition and electron density interpretation. Refinement of structures is dealt with starting from the classical least squares approach and subsequently moving to maximum likelyhood methods. Finally, the different techniques used to validate crystal structures during and after refinement are covered. Attention is given to how and in what detail crystal structures can be interpreted.
During the practicals, the student will determine the crytal structure of a small protein starting from data collection (in house or if possible at a synchrotron source) and ending with a finalized structure. The exact project will vary and depend on the structural biology projects that are tackled within the research team.
Participation during the practicals is obligatory.
Power point slides and lecture notes are made avaiable via the on-line learning platform.
- The student is knowledgeable on the different steps that are required to determine the structure of a macromolecule via X-ray crystallography.
- The student knows the relationship between an atomic model, an electron density map, structure factors and a measured diffraction pattern.
- The student can understand a paper dealing with structure determination of a macromolecule by X-ray crystallography and can assess the quality of the crystal structure that is described therein.
-The student has theoretical and practical knowledge on and understands the different methods that are used to determine as well as improve the structure factor phases that are used for the calculation of an electron density map
- The student knows the different concepts regarding crystal symmetry (point groups, space groups, crystal lattices) that are relevant for macromolecular crystallography and knows how symmetry in real space is related to symmetry in reciprocal space
- The student has theoretical and practical knowledge on the principles on which refinement of macromolecular structures is based and how this process is validated.
- The student knows and can explain the theoretical background behind crystallization processes of macromolecules and can list and explain the strategies that are used to improve initial crystallization hits.
- The student knows how to assess the quality of a diffraction pattern, knows the methods that can be used to improve crystal, diffraction and knows the strategies that are used to optimally collect a dataset. The student has practical knowledge on the processing of an X-ray dataset.
The final grade is composed based on the following categories:
Oral Exam determines 100% of the final mark.
Within the Oral Exam category, the following assignments need to be completed:
Oral examination with written preparation of three or four open questions, covering multiple parts of the course. Both knowledge and insight are probed. There is no separate examination of the practicals. This part is included in the oral examination.
This offer is part of the following study plans:
Master of Bioengineering Sciences: Cell and Gene Biotechnology: Medical Biotechnology (only offered in Dutch)
Master of Bioengineering Sciences: Cell and Gene Biotechnology: Molecular Biotechnology (only offered in Dutch)
Master of Bioengineering Sciences: Cell and Gene Biotechnology: Agrobiotechnology (only offered in Dutch)
Master of Bioengineering Sciences: Chemistry and Bioprocess Technology: Food Biotechnology (only offered in Dutch)
Master of Bioengineering Sciences: Chemistry and Bioprocess Technology: Chemical Biotechnology (only offered in Dutch)
Master of Bioengineering Sciences: Chemistry and Bioprocess Technology: Biochemical Biotechnology (only offered in Dutch)