NKEB13008U Crystallography - BSc

Volume 2024/2025

BSc Programme in Biochemistry
BSc Programme in Chemistry


Crystallography is the main technique by which the three-dimensional structures of molecules are determined. One advantage of crystallography is that similar methods can be used to determine the structure of molecules ranging in size from just a few atoms to the size of ribosomal particle (in the MDa range). The aim of this course is to provide the student with fundamental knowledge about the crystallographic methods used to determine the structure of crystalline materials, especially single crystals of bio-macromolecules (primarily proteins) and small molecules, covering the main aspects of chemical and macromolecular crystallography from crystallization to structure validation, structural databases, use of large-scale X-ray and neutron facilities and touching on state-of-the-art methods (fragment screening, serial crystallography, electron crystallography). The theoretical knowledge will be reinforced by exercises, including numerical exercises. The students will be introduced to laboratory and computational methods including specialized software and databases used in the field, increasing their digital competences.

Much of the theory is common to macromolecular and chemical crystallography, and for the more specific lectures, equal weight is given to protein crystallography and crystallography of smaller molecules.The students will also gain experience in some practical aspects of crystallization and crystallographic structure determination, through laboratory and computer-based practical classes. The practical classes cover 1) crystallization of a protein; 2) crystallization, data processing through to structure determination, refinement and analysis of an organic salt; 3) molecular replacement phasing and initial refinement of a protein from given data. A lot of weight is also given to training in critical reading, presentation and discussion of original articles where crystallographic methods are used in a variety of contexts, including medicinal chemistry and biotechnology, for example understanding and improving enzymes used in industry for biosustainable applications.

If your study plan allows it, you are welcome to take this course as a MSc student. This is particularly advisable if you want a general introduction to crystallography, rather than intending to apply what you learn immediately to a project.

Learning Outcome


 The students must demonstrate knowledge of:

  • Crystallization and diffraction theory
  • Crystal symmetry
  • Crystallographic structure determination methods
  • Structure validation



The student must be able to:

  • carry out, under guidance, crystallographic experiments and data analysis, such as crystallization, data processing and simple structure determinations using appropriate software, evaluate their results and describe them in writing
  • determine crystallographic space groups from diffraction data
  • read, critically evaluate and explain original articles in English, where crystallography is used as a main method
  • make use of selected crystal structure databases for structural comparison and to evaluate structure quality
  • solve simple quantitative problems in crystallography, e.g. related to diffraction theory



The students must be able to

  • Analyze and present selected type of data from crystallization and crystallographic experiments
  • Evaluate and discuss crystallization and crystallographic data and the derived structural information based on primary literature and/or database information

Reading material from different textbooks and articles will be used. Eg from

  • W. Massa, Crystal structure determination 2nd edition 2004, Springer-Verlag ISBN: 3-540-20644-2;
  • D. Blow, Outline of Crystallography for Biologists, 2002, Oxford University Press, ISBN: 0-19-851051-9;
  • Gregory S. Girolami, X-ray Crystallography, 2015, University Science Books, ISBN13: 9781891389771;
  • Rhodes, Crystallography made crystal clear, 2006, Academic Press, ISBN: 9780125870733.


Please consult Absalon up to the course to see advice on which textbook to buy (you should not buy them all!). Additional notes, reviews and articles will be available on Absalon.

It is expected that the students are familiar with the content of the courses in introductory maths, chemistry and/or biochemistry at a level expected for first or second year Chemistry or Biochemistry students
The course consists of a theoretical part (lectures, exercise classes and presentation/discussion of original articles) and a practical part (laboratory and computer-based practical sessions). The theoretical part is supported by compulsory electronic quizzes. The practical sessions are also compulsory. In the latter weeks the course maybe supplemented with lectures on specialized topics, voluntary practical classes and/or a visit to the MAX IV synchrotron.
The course is very suitable for Chemistry, Biochemistry and NanoScience students. Students from other disciplines are recommended to contact the teacher before registering in order to discuss their background knowledge as compared to the level of the course.
The course cannot be taken if the Crystallography MSc course has already been taken.
The course gives the necessary background to take on a Project outside course scope, BSc or MSc project in crystallography.
  • Category
  • Hours
  • Lectures
  • 24
  • Class Instruction
  • 6
  • Preparation
  • 140
  • Theory exercises
  • 8
  • Practical exercises
  • 18
  • Excursions
  • 4
  • Guidance
  • 5
  • Exam
  • 1
  • Total
  • 206
Continuous feedback during the course of the semester
7,5 ECTS
Type of assessment
Oral examination, 20-30 minutes
Type of assessment details
Students are allowed to look briefly (2 mins) at short lists of key points they may have prepared at home before they start their answering (see section on aids). No other preparation time is allowed.
Exam registration requirements

The students must have actively participated in the practical classes (80% compulsory attendance) and written short group reports satisfactorily describing the results from their experiments. Additionally the students must have satisfactorily presented 1-2 original articles (individually or in small groups) and satisfactorily completed all compulsory electronic quizzes during the course.

Only certain aids allowed

The students are allowed to look briefly at short lists of key points they may have prepared at home, once they find out which main topics are to be covered in their oral examination (lottery drawn). They are also allowed to look up information in appropriate tables in the textbooks or International tables provided at the oral exam. No other aids are allowed.

Marking scale
7-point grading scale
Censorship form
No external censorship
Several internal examiners

Same as ordinary exam.
All electronic quizzes must have been satisfactorily completed. If the student has not participated in compulsory article presentation, a powerpoint must be handed in. If the student has not participated in 80% of practical classes, completion of 80% of the practical work will have to be carried out as self-study. Only minimal supervision can be expected and only when justified by safety considerations. All exam requirements must be satisfied latest three weeks before the re-examination, and the student must contact the responsible teacher at least four weeks before the re-examination, to agree on the necessary practical details.

Criteria for exam assesment

See 'learning outcome'