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Introduction to Macromolecular X-ray Crystallography Biochem 300 Borden Lacy Print and online resources: Introduction to Macromolecular X-ray Crystallography, by Alexander McPherson Crystallography Made Crystal Clear, by Gale Rhodes http://www.usm.maine.edu/~rhodes/CMCC/index.html http://ruppweb.dyndns.org/Xray/101index.html Online tutorial with interactive applets and quizzes. http://www.ysbl.york.ac.uk/~cowtan/fourier/fourier.html Nice pictures demonstrating Fourier transforms http://ucxray.berkeley.edu/~jamesh/movies/ Cool movies demonstrating key points about diffraction, resolution, data quality, and refinement. http://www-structmed.cimr.cam.ac.uk/course.html Notes from a macromolecular crystallography course taught in Cambridge Practical Applications of X-ray Crystallography Crystal -> Diffraction pattern -> Electron density -> Model Spacegroups, obtaining crystals Data collection and related statistics Evaluating structures and reading structure papers What can you see and learn with this method? What else can you do? The Crystal Lattice The Crystal Lattice The Seven Crystal Systems The 14 Bravais Lattices Crystals and the asymmetric unit: Rotational Symmetry Operators: Rotational Symmetry Operators: Translational Symmetry Operators: Translational Symmetry Operators: How are molecules packed within the lattice? How to obtain crystals: Work with sample that you expect will be structured. Obtain pure, homogeneous sample at high concentration Bring your sample solution to supersaturation to allow for spontaneous nucleation by varying the pH, temperature, and/or concentration of salt, precipitant, and/or organic solvent. Allow crystals to grow. mosaicity Techniques for super-saturation and growth Batch crystallization Liquid-liquid diffusion Dialysis Vapor-diffusion: Hanging drop or sitting drop QuickTime™ and a TIFF (LZW) decompressor are needed to see this picture. Once you have crystals.. Are they what you want? Do they diffract? Can they be cryo-cooled? Data processing Determine your space group. Index and integrate. h,k,l, I Merge partial reflections, determine scale factors that minimize differences between identical reflections collected on different frames, and average the intensities of symmetrically identical reflections. h,k,l, I, s Assessing data quality Completeness, redundancy, signal-to-noise (I/s), how well do different frames of data agree after scaling (Rmerge)? How do these statistics look for the high-resolution data? How good are your maps? Molecule-solvent separation Continuous density, secondary structure Features consistent with the resolution of the data ( ex. side chains, ordered water) Can you omit pieces of the model and still see them due to your phases? What does resolution mean in practice? 6.0 Å 4.5 Å 3.0 Å 1.6 Å Criteria for judging a structure R-factor and Rfree Deviation from ideal bond lengths and angles Distribution of y and f peptide bond torsion angles Ramachandran Plot Consistency with previously determined structures Chemical and biological sense What else can you do? Membrane proteins Complexes Drug design Structural genomics Laue diffraction and time resolved crystallography Neutron diffraction Metallochemistry with XAFS Small angle x-ray scattering Fiber diffraction