Crystal structure determination

X-ray crystallography VS NMR are complementary techniques NMR X-ray crystallography ________________________________________________________________ short time scale, protein folding long time scale, static structure solution, purity single crystal, purity < 20kD, domain any size, domain, complex functional active site active or inactive domains domains atomic nuclei, chemical bonds electron density resolution limit 2-3.5Å resolution limit 2-3.5Å primary structure must be known primary structure must be know

Bragg's Law X-ray difraction W.H.Bragg 1912. An X-ray which reflects from the surface of a substance has travelled less distance than an X-ray which reflects from a plane of atoms inside the crystal. The penetrating X-ray travels down to the internal layer, reflects, and travels back over the same distance before being back at the surface. The distance travelled depends on the separation of the layers and the angle at which the X-ray entered the material. For this wave to be in phase with the wave which reflected from the surface it needs to have travelled a whole number of wavelengths while inside the material. Bragg expressed this in an equation now known as Bragg's Law: Bragg's Law X-ray difraction W.H.Bragg 1912. When n is an integer (1, 2, 3 etc.) the reflected waves from different layers are perfectly in phase with each other and produce a bright point on a piece of photographic film. Otherwise the waves are not in phase, and will either be missing or feint.

http://www-outreach. phy. cam. ac http://www-outreach.phy.cam.ac.uk/camphy/xraydiffraction/xraydiffraction_exp.htm

William Bragg's spectrometer The first ionization spectrometer designed and constructed by William Henry Bragg in 1912-13, used to measure variations in scattering angles of crystals in order to determine their structures. This is the basis of Crystallography. Date 1912 Place made Leeds

X-ray Charcterisation CRYSTALS program 2000 X-ray Charcterisation

Kappa CCD diffractometer

The electron density map crystal colecting X-ray ekspozer Difraction picture phase The electron density map filtration structural model procesing

MODELING The position of these beams is related to the What are we trying to find? The position of these beams is related to the periodicity of the electron density. The intensity is related to the electron density

What's the first get, and FINALLY WHAT WE WANT : lots and lots of numbers picture CIF file

Import cif Cif file Publish file CIF data

Exchange of Results This is usually done via text (ASCII) files. A program is needed to convert the data into pictures and tables • Cif files: Crystallographic Information File format. This has become an international standard. • SHELX files: After the name of a widely used crystallographic program. • PDB files: Protein Data Bank format. Often used by modelling and graphics programs.

Graphics Programs-picture There are dozens available from free viewers to expensive modelling packages Mercury: Free from CCDC. Has some knowledge of symmetry operations. Reads cif files. Will output bitmap files. Encifer: Free from CCDC. As above, but also enables you to read, edit and validate the syntax of cif files. Only outputs cif files. Ortep: Free with WINGX. A fully functional crystallographic plotting program. Reads cif and SHELX file.

CHECKCIF

CCDC – The Cambridge Crystallographic Data Centre CCDC maintains and distributes the CSD (Cambridge Structural Database), plus software for searching, viewing and analysing crystal structures.

Uses of X-ray Crystallography • Gross structure – atom types and Connectivity • Stereo chemistry • Fine detail – bond lengths, angles and torsion angles • Electron density distributions • Crystal Structure

High Quality Crystals

DATA COLLECTION Stages: 1. Crystal selection. Get the best you can 2. Crystal mounting. Usually oil-drop method 3. Unit cell determination. Often automatic 4. Main data collection.

position