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Crystallography Course 2013

Lectures

Lecture Presentations

Molecular replacement (pdf)
03 Protein Expression Crystallization And Mutagenesis – Meindert Lamers (pdf)
08 Maximum Likelihood Experimental Phasing Isomorphous Replacement And Anomalous Scattering – Airlie McCoy (pdf)
CCP4MG (pdf)
Diffraction Geometry • Diffraction from a crystal – Laue equations • Reciprocal lattice • Ewald construction • Data collection strategy (pdf)
Experimental phasing, Pattersons and SHELX (pdf)
Integration and Scaling Harry Powell MRC LMB Crystallography Course 10th May 2013 (pdf)
Introduction to X-ray crystallography Jan Löwe MRC Laboratory of Molecular Biology (pdf)
Introduction to X-ray diffraction • Waves • Diffraction • Structure factors • Reciprocal space (pdf)
LMB Crystallography Course, 2013 (pdf)
Model-Building of Proteins Using X-ray Data With Coot Paul Emsley (pdf)
Refinement Garib N Murshudov MRC-LMB Cambridge (pdf)
Twinningàandàotheràpathologiesà AndreyàLebedevà à (pdf)
14 Making Pretty Pictures Of Macromolecules – Meindert Lamers (pdf)
Automated phase improvement and model building Kevin Cowtan cowtan@ysbl.york.ac.uk (pdf)

Tutorials

Data Processing and Scaling – Phil Evans and Andrew Leslie

Molecular Replacement – Airlie McCoy

Experimental Phasing – Andrea Thorn

Refinement  – Rob Nicholls, Fei Long and Garib Murshudov

Literature

Recommended Reading – General:

Blundell T.L. & Johnson L. “Protein Crystallography” (1976)
Very good book that describes protein crystallography, starting from crystallisation, covering almost all techniques available by 1976. This book is highly recommended if you can find it.
Rupp B. “Biomolecular Crystallography: Principles, Practice, and Application to Structural Biology” (2009)
The latest and most recommended book on crystallography for the biologist and/or practical crystallographer. It has a good description of the mathematical and physical basis of macromolecular crystallography.
Blow D. “Outline of Crystallography for Biologists” (2002)
This book is meant to be a very readable introduction to crystallography. For biologists (or readers from any field) using X-ray crystallography as a method, perhaps this book should be one of the first you read.
Drenth J “Principles of Protein X-ray Crystallography” (2007)
This book has math just enough to understnd crystallography. If you are considered to do serious X-ray crystallpgraphy then this book would serve as very useful starting point.
James R.W. “The Optical Principles of the Diffraction of X-rays” (1948)
A comprehensive exposition of diffraction theory. It has very good mathematical description of diffraction geometry, intensity of reflections, atomic scattering factors, anomalous scattering etc. The book may be a bit heavy on maths, but if you can read it through then you may know everything about X-ray crystallography and more.
Vainshtein B.K. “Modern Crystallography. Vol 1, Fundamentals of Crystals, Symmetry and Methods of Structural Crystallography” (1994)
This book is a bit heavy on the maths side. It has a very nice account of symmetry and space groups, and gives a mathematical reason why there are a limited number of point groups (32) and spaces groups (230). This book should be used as a reference.
Srinavasan R. & Parthasarathy S. “Some Statistical Applications in X-ray Crystallography” (1976)
This book describes statistical distributions of structure factor amplitudes. It also gives derivations of many distributions used in modern macromolecular crystallography (e.g. Rice distribution, although they do not call it the Rice distribution; Wilson distribution; joint distributions of related crystals). A bit heavy on the maths side.

Recommended Reading – Protein Expression, Crystallization and Mutagenesis:

Ligation Independent Cloning:
Aslanidis C. & de Jong P.J. (1990) Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Research 18(20), 6069-74.
Protein Expression:
Studier F.W. (2005) Protein production by auto-induction in high density shaking cultures. Protein Expression and Purification 41, 207-34.
Protein Enginering:
Derewenda Z.S. (2010) Application of protein engineering to enhance crystallizability and improve crystal properties. Acta Crystallographica D: Biological Crystallography 66(5), 604-15.
SERp server http://services.mbi.ucla.edu/SER/
Protein Freezing For Storage:
Deng J. et al. (2004) An improved protocol for rapid freezing of protein samples for long-term storage. Acta Crystallographica D: Biological Crystallography 60, 203-4.
Hanging Drop Diffusion:
Diller D.J. & Hol W.G. (1999) An accurate numerical model for calculating the equilibration rate of a hanging-drop experiment. Acta Crystallographica D: Biological Crystallography 55(3), 656-63.
Cryo Crystallography:
Garman E.F. & Schneider T.R. (1997) Macromolecular cryocrystallography. Journal of Applied Crystallography 30, 211-37.
Warkentin M., Berejnov V., Husseini N.S. & Thorne R.E. (2006) Hyperquenching for protein cryocrystallography. Journal of Applied Crystallography 39, 805-11.
Pellegrini E., Piano D. & Bowler M.W. (2011) Direct cryocooling of naked crystals: are cryoprotection agents always necessary? Acta Crystallographica D: Biological Crystallography 67, 902-6.
Russi S. et al. (2011) Inducing phase changes in crystals of macromolecules: status and perspectives for controlled crystal dehydration. Journal of Structural Biology 175, 236-43.

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