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Course module: SK-MBPPC
SK-MBPPC
Applied Protein Crystallography
Course infoSchedule
Course codeSK-MBPPC
ECTS Credits3
Category / LevelM (Master)
Course typeCourse
Language of instructionEnglish
Offered byFaculty of Science; Graduate School of Life Sciences; Graduate School of Life Sciences;
Contact persondr. E.G. Huizinga
Telephone+31 30 2532866
E-maile.g.huizinga@uu.nl
Lecturers
Contactperson for the course
dr. E.G. Huizinga
Other courses by this lecturer
Lecturer
dr. E.G. Huizinga
Other courses by this lecturer
Lecturer
dr. B.J.C. Janssen
Other courses by this lecturer
Lecturer
dr. M.H. Lutz
Other courses by this lecturer
Teaching period
JAAR  (03/09/2018 to 29/08/2019)
Teaching period in which the course begins
JAAR
Time slot-: Not in use
Study mode
Full-time
RemarkPeriod: October 29 - November 9 Registration
Through the course coordinator (Dr. E.G. Huizinga, e.g.huizinga@uu.nl)
Enrolment periodfrom 28/05/2018 up to and including 24/02/2019
Enrolling through OSIRISNo
Enrolment open to students taking subsidiary coursesYes
Pre-enrolmentNo
Waiting listNo
Aims
At the end of the course, you should be able to:
 
  • Perform all steps of a standard protein crystal structure determination by molecular replacement using the crystallographic software package CCP4.
  • Interpret relevant quality indicators in each step of the structure determination process.
  • Evaluate the quality of published models from protein crystallography.
  • Judge whether a conclusion based on a crystal structure is justified considering the quality of the diffraction data.
Content
X-ray diffraction on protein crystals is a powerful technique to determine structures of large biomolecules at (near) atomic resolution. Technological and methodological advances and the vast and steadily increasing number of protein structures already available, enable rapid determination of protein structures by the method of molecular replacement, provided that suitable diffracting crystals can be obtained and the structure of a >25% homologous protein is available. In this hands-on course you will determine a protein crystal structure yourself using molecular replacement. You will perform all steps from diffraction data processing to validation and analysis of the refined model.
The objectives of the course are two-fold: firstly to learn how to obtain the best possible protein model by making informed decisions on the basis of relevant quality indicators throughout the structure determination process. Secondly, to learn how to critically judge the quality of protein structures from the protein data bank and their suitability as a starting point for further research. In fact solving a protein structure yourself is an excellent way to appreciate the strengths and pitfalls of protein crystal structures. The course aims at students that wish to be able to determine crystals structures themselves as well as students that wish to be able to use the wealth of information that protein structures provide in a critical fashion. The underlying physics and mathematics of X-ray crystallography will be dealt with in a qualitative manner and only for as far it is relevant for the quality of the final protein model. A typical course day consists of a lecture, computer practical (with and without guidance), and student presentations about the progress of their structure determinations.
 
 
Entry requirements
Prerequisite knowledge
Students must know the basics of protein structure and be acquainted with basic concepts of (protein) crystallography.
Specifically, students must be familiar with: Bragg’s law; Lattice planes; Reciprocal space; Ewald construction; Representation of waves as complex numbers; Argand diagrams; Electron density; Fourier transformation (qualitatively), Patterson function (qualitatively).
Private study materials
Prerequisite knowledge can be acquired by attending the bachelor course “Röntgen Diffractie en EM” (SK-B2RDEM) or through self-study of the reader accompanying SK-B2RDEM. Better suited for self-study is the book “Crystallography Made Crystal Clear; a Guide for Users of Macromolecular Models” (chapters 1-5 and chapter 6 pages 109-116).
Upon request question-answer sessions will be organized to help students with acquiring the prerequisite knowledge prior to the start of the course.
Required materials
-
Recommended materials
Book
Crystallography Made Crystal Clear by Gale Rhodes (Third Edition; ISBN: 978-0-12-587073-3). The chapters of this book are available as pdf files through the Utrecht University library.
Instructional formats
Computer practical

Lecture

Lecture/seminar

Presentation

Tests
Final result
Test weight100
Minimum grade-

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Kies de Nederlandse taal