Course syllabus for BIOC 530 section on X-ray Crystallography 2017

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Date      Lecture On-line Material
3 Oct
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
Bragg's Law (Wikipedia page) (java applet)
Escher Web Sketcher (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
5 Oct
Reciprocal Space ⇔ Real Space
• Fourier Transforms
• Point A - Experimental data (Reciprocal Space)
• Point B - Electron density maps (Real Space)
• The Phase Problem
how to get from point A to point B?

Kevin Cowtan's Book of Fourier
Fourier Series in 1D
Java applet
non-Java applet
Fourier Series in 2D
Structure Factor Tutorial
24 Oct
The Phase Problem
We only measured half of what we needed???
Structure Determination - Solving the Phase Problem
Molecular Replacement
Direct Methods
MIR (Multiple Isomorphous Replacement)
Anomalous Scattering (MAD SAD SIRAS)
What do we learn from crystal structures?
Model-building - what goes in, what comes out
How to refine a model
How not to refine a model

X-ray Anomalous Scattering
26 Oct
How to judge the quality of a crystal structure
• Criteria
• Validation tools
Where to find a crystal structure
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
wwPDB Validation Reports
PDB Redux (a.k.a. PDB REDO)
Cool Stuff
Free Electron Laser (Stanford) (Youtube video)

Class Notes

2018 class notes (PDF) (updated 24 Oct 2018)

Homework Assignments (Email me if you have questions)

Part 1 (lectures 1 + 2) should be available on the class web site. Part 2 (lectures 3 + 4) should be available on the class web site.

Links to on-line material from Crystallography courses taught elsewhere


Ethan A Merritt (HSB 428b)