Course syllabus for BIOC 530 Crystallography Section

Date	Lecture	On-line Material
25 Sep	Why X-rays? Why Crystals? • Bragg's Law • What's in a crystal? space group symmetry, non-crystallographic symmetry, impossible symmetry • Practical Details growing crystals, sample preparation, X-ray sources, data collection	Crystals Bragg's Law (Wikipedia page) (java applet) Penrose Tilings and the 2011 Nobel Prize Crystal Growth 101 (PDF) Phase Diagrams - theory of crystallization Synchrotron Radiation Videos What's a Synchrotron? Student Data Collection Trip to APS Students stay home - robot does the work
27 Sep	Reciprocal Space ⇔ Real Space • Fourier Transforms • Point A - Experimental data (Reciprocal Space) • Point B - Electron density maps (Real Space) • How to get from point A to point B? The Phase Problem We only measured half of what we needed?!! Structure Determination - Solving the Phase Problem Molecular Replacement Other methods (brief overview only)	Kevin Cowtan's Book of Fourier Fourier Series in 1D Java applet non-Java applet Fourier Series in 2D Structure Factor Tutorial Ways to solve the Phase Problem X-ray Anomalous Scattering
30 Sep	What you can see in an electron density map Strengths and Limitations of Crystallography Difference Fourier Maps Finding the missing piecese Ligands / Active Sites / Drug Design Model-building - what goes in, what comes out How to refine a model How not to refine a model	Example of fitting a ligand to difference density
23 Oct	How to judge the quality of a crystal structure • Criteria • Validation tools Where to find a crystal structure www.rcsb.org Frontiers of Crystallography • Nanocrystals and femtosecond experiments	Validation Criteria The geometry of basic protein elements Braille for Pugilists Essay from 20 years ago but still good reading Validation Tools Molprobity wwPDB Validation Reports PDB Redux (a.k.a. PDB REDO) Cool Stuff Free Electron Laser (Stanford) (Youtube video)

Class Notes

Homework Assignments (Email me if you have questions)

Part 1 (lectures 1 - 3) and Part 2 (lecture 4) will be available on the class web site.

Links to on-line material from Crystallography courses taught elsewhere

This material is not required reading, but is a good place to start if you want to pursue ideas presented in class in more depth. The first link in particular is nice because it parallels the material covered in BIOC 530.

Overview of Protein Crystallography Course: Randy Read (MRC Cambridge) Excellent introductory page, followed by a lot of more advanced topics
Interactive Diffraction Tutorial (MSU mirror): T.H. Proffen (LANL) and R.B. Neder (Würtzburg)
Interactive Structure Factor Tutorial: Kevin Cowtan (York)
Anomalous Scattering (MAD Phasing): One way to overcome the phase problem
"Ramachandran and his Map" reprint from Resonance Oct 2001. ( original source): Historical explanation (quite readable).
Model validation tutorial for an EBI course (Gerard Kleywegt)

Course syllabus for BIOC 530 section on X-ray Crystallography 2019

Class Notes

Homework Assignments (Email me if you have questions)

Links to on-line material from Crystallography courses taught elsewhere

This material is not required reading, but is a good place to start if you want to pursue ideas presented in class in more depth. The first link in particular is nice because it parallels the material covered in BIOC 530.

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