X-ray crystallography

X-ray crystallography is a technique in crystallography in which the pattern produced by the diffraction of x-rays through the closely spaced lattice of atoms in a crystal is recorded and then analyzed to reveal the nature of that lattice. The spacings in the crystal lattice can be determined using Bragg's law. The electrons that surround the atoms are the entities which physically interact with the incoming X-ray photons to diffract them, not the atomic nuclei.

The material and molecular structure of a substance can often be inferred by quantitative study of this pattern. It is widely used in chemistry and biochemistry to determine the structures of an immense variety of molecules, including inorganic compounds, DNA and proteins.

Inorganic Structures

X-ray diffraction finds frequent use in materials science because sample preparation is relatively easy, and the test itself is often rapid and non-destructive. The vast majority of engineering materials are crystalline, and even those which are not yield some useful information in diffraction experiments.

The pattern of diffraction peaks can be used to quickly identify materials (thanks to the JCPDS pattern database), and changes in peak width or position can be used to determine crystal size, purity, and texture.

Organic Structures

The first protein crystal structure was of sperm whale myoglobin, as determined by Max Perutz and Sir John Cowdery Kendrew in 1958, which led to a Nobel Prize in Chemistry. The X-ray diffraction analysis of myoglobin was originally motivated by the observation of myoglobin crystals in dried pools of blood on the decks of whaling ships.

X-ray crystallography played a major role in elucidating the double-helix structure of DNA. See Rosalind Franklin, James D. Watson, Francis Crick. Today X-ray crystallography is often used to determine how drugs, such as anti-cancer medications, can be improved to better influence their protein targets.

The molecule must be crystallized because one photon diffracted by one electron cannot be reliably detected. However, because of the regular crystalline structure, the photons are diffracted by corresponding electrons in many symmetrically arranged molecules. Because waves of the same frequency whose peaks match reinforce each other, the signal becomes detectable.

To determine a structure, one must first grow crystals of the molecule of interest using some method of crystallization. This can be a painstaking procedure for macromolecules such as protein and DNA complexes. The crystals are harvested and often frozen with liquid nitrogen. Freezing crystals both reduces radiation damage incurred during data collection and decreases thermal motion within the crystal. Crystals are placed on a diffractometer , a machine that emits a beam of x-rays. The x-rays diffract off the electrons in the crystal, and the pattern of diffraction is recorded on film and scanned into a computer. These diffraction images are combined and eventually used to construct a map of the electron density of the molecule that was crystallized, atoms are then fit to the electron density map and various parameters such as position are refined to best fit the observed diffraction data.

It is important to note that even after obtaining crystals suitable for diffraction analysis, current X-ray sources and detectors limit the measurement of only the diffracted photon intensities and not their respective phases, the latter encoding the majority of the information about the actual shape of electron density. A combination of experimental and computational methods are typically used to solve the phase problem, in order to estimate phases and obtain an initial map of the electron density.

After phases are estimated, a model made up of atoms is built and refined against the observed data. Once a model of a molecule's structure has been determined, it is often deposited in a crystallographic database such as the Protein Databank or the Cambridge Structure Database. Many structures obtained in private commercial ventures to crystallize medicinally relevant proteins, are not deposited in public crystallographic databases.

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See also

• diffractometer
• Fourier transform
• molecular model
• Patterson function
• reciprocal space
• space group
• phase problem
• Bragg's law

Paper Resources/Books

Drenth J. Principles of Protein X-Ray Crystallography. Springer-Verlag Inc. NY: 1999, ISBN 0387985875.

Glusker JP, Lewis M, Rossi M. Crystal Structure Analysis for Chemists and Biologists. VCH Publishers. NY:1994, ISBN 0471185434.

Rhodes G. Crystallography Made Crystal Clear. Academic Press. CA: 2000, ISBN 0125870728.