Introduction to Macromolecular X-ray Crystallography Biochem 300 Borden Lacy Print and online resources: Introduction to Macromolecular X-ray Crystallography,

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Presentation transcript:

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 Online tutorial with interactive applets and quizzes. Nice pictures demonstrating Fourier transforms Cool movies demonstrating key points about diffraction, resolution, data quality, and refinement. Notes from a macromolecular crystallography course taught in Cambridge

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? Crystal -> Diffraction pattern -> Electron density -> Model Practical Applications of X-ray Crystallography

The Crystal Lattice

The Seven Crystal Systems

The 14 Bravais Lattices

Crystals and the asymmetric unit:

Rotational Symmetry Operators:

Translational Symmetry Operators:

How are molecules packed within the lattice?

How to obtain crystals: 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 Work with sample that you expect will be structured.

Techniques for super-saturation and growth Batch crystallization Liquid-liquid diffusion Dialysis Vapor-diffusion: Hanging drop or sitting drop

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. 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,  h,k,l, I

Assessing data quality Completeness, redundancy, signal-to-noise (I/  ), 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 R free Deviation from ideal bond lengths and angles Distribution of  and  peptide bond torsion angles Consistency with previously determined structures Chemical and biological sense Ramachandran Plot

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