Biophysics 602: Principles of Macromolecular Crystallography1
Winter 2011
This course provides an in-depth treatment of the theory and practice of determining macromolecular
structure by X-ray crystallography. Three credit hours. Grades will be based on homework and two
exams.
The class will meet Tuesdays and Thursdays from 3:00–4:30 pm in room 6311 Medical Sciences I.
Lecture notes should be available on the CTools site the day before class. Please print them and bring to
class.
Class schedule
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
1
Thu
Tue
Thu
Tue
Thu
Tue
Thu
Tue
Thu
Tue
Thu
Tue
Thu
Tue
Thu
Tue
Thu
Tue
Thu
Tue
Thu
Tue
Thu
Tue
Thu
Tue
Thu
Tue
Thu
Tue
Fri
Jan 06
Jan 11
Jan 13
Jan 18
Jan 20
Jan 25
Jan 27
Feb 01
Feb 03
Feb 08
Feb 10
Feb 15
Feb 17
Feb 22
Feb 24
Mar 01
Mar 03
Mar 08
Mar 10
Mar 15
Mar 17
Mar 22
Mar 24
Mar 29
Mar 31
Apr 05
Apr 07
Apr 12
Apr 14
Apr 19
Apr 22
Crystal Geometry
Space Groups and Reciprocal Lattice
X-ray Scattering and Diffraction Geometry
Reciprocal space and Friedel's law
Electron Density, Phase Problem
Instrumentation, Data Collection
Statistics & Probability
Experimental phasing, Patterson methods
Isomorphous replacement
Anomalous phasing
Heavy atom refinement (tentative)
Review
Mid-term Exam
NO CLASS - Winter Recess
NO CLASS - Winter Recess
Improving maps
Crystallization: theory and technology
NCS & Molecular Replacement
NCS & Molecular Replacement
NCS & Molecular Replacement
Density interpretation and Model building
Refinement
Refinement
Structure Validation
Structure analysis
Crystal Twinning
TBD
TBD
Second Exam
PDF file of this document is available on CTools site http://ctools.umich.edu
Tesmer
Tesmer
Tesmer
Tesmer
Tesmer
Saper
Saper
Saper
Saper
Saper
Saper
Saper
Saper
Saper
Saper
Trievel
Saper
Saper
Saper
Tesmer
Tesmer
Tesmer
Tesmer
Tesmer
Saper
TBD
TBD
Chapter[.section]
5.1–5.2
5.3–5.7
6.1–6.3
6.4–6.6
9.1–9.3
8.1–8.3, 8.5
7
9.4–9.5, 10.1–10.3
6.4, 10.4–10.5
10.6
10.7
3, 4
11
11
11
12.1
12.2
12.3
13.1-13.3
13.4-13.10
Syllabus – Biophysics 502, Winter 2010
2
Instructors :
Mark Saper
John Tesmer
Raymond Trievel
3040 Chemistry
3435 Life Sciences Inst
4301C MSRB III
(734) 764 3353
(734) 615-9544
(734) 647-0889
saper@umich.edu
tesmerjj@umich.edu
rtrievel@umich.edu
Textbook:
†Rupp B. (2009). Biomolecular crystallography: Principles, Practice, and Application to Structural
Biology. Garland Science, New York, NY.
Other Textbooks/Resources:
*Blow, D. M. (2002). Outline of crystallography for biologists. Oxford University Press, New York
Good overview with more advanced material in grey boxes.
*†Drenth, J. (2007 or 1999). Principles of protein x-ray crystallography. Springer, New York (3rd or
2nd edition)
Complete description of all techniques with mathematical treatment.
Entire book available online in PDF format (no charge):
http://www.springerlink.com.proxy.lib.umich.edu/content/mj2356/
Also available in paperback at discounted price of $24.95 (includes shipping, 8–11 days):
http://www.springerlink.com.proxy.lib.umich.edu/content/mj2356/mycopy/
International tables for crystallography volume F: Crystallography of biological macromolecules. E.
Arnold, M. G. Rossmann, Eds. (Kluwer, Dordrecht, Netherlands, 2001).
Full-text online: http://www.springerlink.com/content/u2h572/?sortorder=asc&v=condensed
Doublié, S. (2007). Macromolecular crystallography protocols, Two volumes. Humana Press.
Available online:
http://proxy.lib.umich.edu/login?url=http://dx.doi.org/10.1007/978-1-59745-209-0
http://proxy.lib.umich.edu/login?url=http://dx.doi.org/10.1385/1597452661
Stout G.H. & Jensen L.H. (1989). X-ray structure determination: a practical guide. Wiley, New York
Rupp, B (2010). Crystallography 101: An Introductory Course.
http://www.ruppweb.org/Xray/101index.html
Rhodes, G. (2006). Crystallography made crystal clear: a guide for users of macromolecular
models. Academic Press, San Diego
Little math.
Blundell, T. L. & Johnson, L. N. (1976). Protein crystallography. Academic Press, New York
Old buy many parts still relevant.
Methods in Enzymology, Volumes 114, 115, 276, 277, 374.
Provides thorough reviews of selected topics in crystallography
* on reserve in Shapiro Library
† on reserve in Taubman Library