X-ray crystallography

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Jump to: navigation, search X-ray crystallography can locate every atom in a zeolite, an aluminosilicate with many important applications, such as water purification. X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and scatters into many different directions. From the angles and intensities of these scattered beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal. From this electron density, the mean positions of the atoms in the crystal can be determined, as well as their chemical bonds, their disorder and various other information. Since very many materials can form crystals such as salts, metals, minerals, semiconductors, as well as various inorganic, organic and biological molecules X-ray crystallography has been fundamental in the development of many scientific fields. In its first decades of use, this method determined the size of atoms, the lengths and types of chemical bonds, and the atomic-scale differences among various materials, especially minerals and alloys. The method also revealed the structure and functioning of many biological molecules, including vitamins, drugs, proteins and nucleic acids such as DNA. X-ray crystallography is still the chief method for characterizing the atomic structure of new materials and in discerning materials that appear similar by other experiments. X-ray crystal structures can also account for unusual electronic or elastic properties of a material, shed light on chemical interactions and processes, or serve as the basis for designing pharmaceuticals against diseases. After a crystal has been obtained or grown in the laboratory, it is mounted on a goniometer and gradually rotated while being bombarded with X-rays, producing a diffraction pattern of regularly spaced spots known as reflections. The two-dimensional images taken at different rotations are converted into a three-dimensional model of the density of electrons within the crystal using the mathematical method of Fourier transforms, combined with chemical data known for the sample. Poor resolution (fuzziness) or even errors may result if the crystals are too small, or not uniform enough in their internal makeup. X-ray crystallography is related to several other methods for determining atomic structures. Similar diffraction patterns can be produced by scattering electrons or neutrons, which are likewise interpreted as a Fourier transform. If single crystals of sufficient size cannot be obtained, various X-ray scattering methods can be applied to obtain less detailed information; such methods include fiber diffraction, powder diffraction and small-angle X-ray scattering (SAXS). In all these methods, the scattering

is elastic; the scattered X-rays have the same wavelength as the incoming X-ray. By contrast, inelastic X-ray scattering methods are useful in studying excitations of the sample, rather than the distribution of its atoms.

Contents
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1 History o 1.1 Early scientific history of crystals and X-rays o 1.2 X-rays analysis of crystals o 1.3 Development from 1912 to 1920 2 Contributions to chemistry and material science o 2.1 Mineralogy and metallurgy o 2.2 Early organic and small biological molecules o 2.3 Protein crystallography 3 Relationship to other scattering techniques o 3.1 Elastic vs. inelastic scattering o 3.2 Other types of X-ray scattering o 3.3 Electron and neutron diffraction 4 Methods o 4.1 Overview of single-crystal X-ray diffraction 4.1.1 Procedure 4.1.2 Limitations o 4.2 Crystallization o 4.3 Data collection 4.3.1 Mounting the crystal 4.3.2 X-ray sources 4.3.3 Recording the reflections o 4.4 Data analysis 4.4.1 Crystal symmetry, unit cell, and image scaling 4.4.2 Initial phasing 4.4.3 Model building and phase refinement o 4.5 Deposition of the structure 5 Diffraction theory o 5.1 Intuitive understanding by Bragg's law o 5.2 Scattering as a Fourier transform o 5.3 Friedel and Bijvoet mates o 5.4 Ewald's sphere o 5.5 Patterson function o 5.6 Advantages of a crystal 6 See also 7 References 8 Further reading o 8.1 International Tables for Crystallography o 8.2 Bound collections of articles

8.3 Textbooks 8.4 Applied Computational Data Analysis 8.5 Historical 9 External links o 9.1 Tutorials o 9.2 Primary databases o 9.3 Derivative databases
o o o o

9.4 Structural validation

[edit] History
[edit] Early scientific history of crystals and X-rays

Drawing of square (Figure A, above) and hexagonal (Figure B, below) packing from Kepler's work, Strena seu de Nive Sexangula. Crystals have long been admired for their regularity and symmetry, but they were not investigated scientifically until the 17th century. Johannes Kepler hypothesized in his work Strena seu de Nive Sexangula (1611) that the hexagonal symmetry of snowflake crystals was due to a regular packing of spherical water particles.[1]

As shown by X-ray crystallography, the hexagonal symmetry of snowflakes results from the tetrahedral arrangement of hydrogen bonds about each water molecule. The water molecules are arranged simiarly to the silicon atoms in the tridymite polymorph of SiO2. The resulting crystal structure has hexagonal symmetry when viewed along a principal axis. Crystal symmetry was first investigated experimentally by Nicolas Steno (1669), who showed that the angles between the faces are the same in every exemplar of a particular type of crystal,[2] and by Ren Just Hay (1784), who discovered that every face of a crystal can be described by simple stacking patterns of blocks of the same shape and size. Hence, William Hallowes Miller in 1839 was able to give each face a unique label of

three small integers, the Miller indices which are still used today for identifying crystal faces. Hay's study led to the correct idea that crystals are a regular three-dimensional array (a Bravais lattice) of atoms and molecules; a single unit cell is repeated indefinitely along three principal directions that are not necessarily perpendicular. In the 19th century, a complete catalog of the possible symmetries of a crystal was worked out by Johann Hessel,[3] Auguste Bravais,[4] Yevgraf Fyodorov,[5], Arthur Schnflies[6] and (belatedly) William Barlow. On the basis of the available data and physical reasoning, Barlow proposed several crystal structures in the 1880s that were validated later by X-ray crystallography;[7] however, the available data were too few in the 1880s to accept his models as conclusive.

X-ray crystallography shows the arrangement of water molecules in ice, revealing the hydrogen bonds that hold the solid together. Few other methods can determine the structure of matter with such sub-atomic precision (resolution). X-rays were discovered by Wilhelm Conrad Rntgen in 1895, just as the studies of crystal symmetry were being concluded. Physicists were initially uncertain of the nature of X-rays, although it was soon suspected (correctly) that they were waves of electromagnetic radiation, in other words, another form of light. At that time, the wave model of light specifically, the Maxwell theory of electromagnetic radiation was well accepted among scientists, and experiments by Charles Glover Barkla showed that X-rays exhibited phenomena associated with electromagnetic waves, including transverse polarization and spectral lines akin to those observed in the visible wavelengths. Singleslit experiments in the laboratory of Arnold Sommerfeld suggested the wavelength of Xrays was roughly 1 Angstrm, one ten millionth of a millimetre. However, X-rays are composed of photons, and thus are not only waves of electromagnetic radiation but also exhibit particle-like properties. The photon concept was introduced by Albert Einstein in 1905,[8] but it was not broadly accepted until 1922,[9][10] when Arthur Compton confirmed it by the scattering of X-rays from electrons.[11] Therefore, these particle-like properties of X-rays, such as their ionization of gases, caused William Henry Bragg to argue in 1907 that X-rays were not electromagnetic radiation.[12] Nevertheless, Bragg's view was not broadly accepted and the observation of X-ray diffraction in 1912[13] confirmed for most scientists that X-rays were a form of electromagnetic radiation.

[edit] X-rays analysis of crystals

The incoming beam (coming from upper left) causes each scatterer to re-radiate a small portion of its energy as a spherical wave. If scatterers are arranged symmetrically with a separation d, these spherical waves will be in synch (add constructively) only in directions where their path-length difference 2d sin equals an integer multiple of the wavelength . In that case, part of the incoming beam is deflected by an angle 2, producing a reflection spot in the diffraction pattern. Crystals are regular arrays of atoms, and X-rays can be considered waves of electromagnetic radiation. Atoms scatter X-ray waves, primarily through the atoms' electrons. Just as an ocean wave striking a lighthouse produces secondary circular waves emanating from the lighthouse, so an X-ray striking an electron produces secondary spherical waves emanating from the electron. This phenomenon is known as elastic scattering, and the electron (or lighthouse) is known as the scatterer. A regular array of scatterers produces a regular array of spherical waves. Although these waves cancel one another out in most directions through destructive interference, they add constructively in a few specific directions, determined by Bragg's law: where d is the spacing between diffracting planes, is the incident angle, n is any integer, and is the wavelength of the beam. These specific directions appear as spots on the diffraction pattern, often called reflections. Thus, X-ray diffraction results from an electromagnetic wave (the X-ray) impinging on a regular array of scatterers (the repeating arrangement of atoms within the crystal). X-rays are used to produce the diffraction pattern because their wavelength is typically the same order of magnitude (1-100 ngstrms) as the spacing d between planes in the crystal. In principle, any wave impinging on a regular array of scatterers produces diffraction, as predicted first by Francesco Maria Grimaldi in 1665. To produce significant diffraction, the spacing between the scatterers and the wavelength of the impinging wave should be roughly similar in size. For illustration, the diffraction of sunlight through a bird's feather was first reported by James Gregory in the later 17th century. The first man-made diffraction gratings for visible light were constructed by David Rittenhouse in 1787, and Joseph von Fraunhofer in 1821. However, visible light has too long a wavelength (typically, 5500 ngstrms) to observe diffraction from crystals. However, prior to the first X-ray diffraction experiments, the spacings between lattice planes in a crystal were not known with certainty. The idea that crystals could be used as a diffraction grating for X-rays arose in 1912 in a conversation between Paul Peter Ewald and Max von Laue in the English Garden in Munich. Ewald had proposed a resonator model of crystals for his thesis, but this model could not be validated using visible light, since the wavelength was much larger than the spacing between the resonators. Von Laue realized that electromagnetic radiation of a shorter wavelength was needed to observe such small spacings, and suggested that X-rays might have a wavelength comparable to the unit-cell spacing in crystals. Von Laue worked with two technicians, Walter Friedrich and his assistant Paul Knipping, to shine a

beam of X-rays through a copper sulphate crystal and record its diffraction on a photographic plate. After being developed, the plate showed a large number of welldefined spots arranged in a pattern of intersecting circles around the spot produced by the central beam.[13][14] Von Laue developed a law that connects the scattering angles and the size and orientation of the unit-cell spacings in the crystal, for which he was awarded the Nobel Prize in Physics in 1914.[15] As described in the mathematical derivation below, the X-ray scattering is determined by the density of electrons within the crystal. Since the energy of an X-ray is much greater than that of an atomic electron, the scattering may be modeled as Thomson scattering, the interaction of an electromagnetic ray with a free electron. This model is generally adopted to describe the polarization of the scattered radiation. The intensity of Thomson scattering declines as 1/m with the mass m of the charged particle that is scattering the radiation; hence, the atomic nuclei, which are thousands of times heavier than an electron, contribute negligibly to the scattered X-rays

Other types of X-ray scattering

X-ray diffraction involves the scattering of X-rays from a single crystal. Other forms of elastic X-ray scattering include powder diffraction, SAXS and several types of X-ray fiber diffraction, which was used by Rosalind Franklin in determining the double-helix structure of DNA. In general, X-ray diffraction produces isolated spots ("reflections"), while the other methods produce smooth, continuous scattering. In general, X-ray diffraction offers more structural information than these other techniques; however, it requires a sufficiently large and regular crystal, which is not always possible to obtain. All of these scattering methods generally use monochromatic X-rays, which are restricted to a single wavelength with minor deviations. A broad spectrum of X-rays (that is, a blend of X-rays with different wavelengths) can also be used to carry out X-ray diffraction, a technique known as the Laue method. This is the method used in the original discovery of X-ray diffraction. Laue scattering provides much structural information with only a short exposure to the X-ray beam, and is therefore used in structural studies of very rapid events (time-resolved X-ray crystallography). However, it is not as well-suited as monochromatic scattering for determining the full atomic structure of a crystal. It is better suited to crystals with relatively simple atomic arrangements, such as minerals. The Laue back reflection mode records X-rays scattered backwards also from a broad spectrum source. This is useful if the sample is too thick or bulky for X-rays to transmit through it. The diffracting planes in the crystal are determined by knowing that the normal to the diffracting plane bisects the angle between the incident beam and the

diffracted beam. A Greninger chart can be used [56] to interpret the back reflection Laue photograph. The X-calibre RTXDB and MWL 110 are commercial systems for Laue back reflection pattern recording. This technique can be used in materials analysis or nondestructive testing.

Methods
[edit] Overview of single-crystal X-ray diffraction

Workflow for solving the structure of a molecule by X-ray crystallography. The oldest and most precise method of X-ray crystallography is single-crystal X-ray diffraction, in which a beam of X-rays strikes a single crystal, producing scattered beams. When they land on a piece of film or other detector, these beams make a diffraction pattern of spots; the strengths and angles of these beams are recorded as the crystal is gradually rotated.[57] Each spot is called a reflection, since it corresponds to the reflection of the X-rays from one set of evenly spaced planes within the crystal. For single crystals of sufficient purity and regularity, X-ray diffraction data can determine the mean chemical bond lengths and angles to within a few thousandths of an ngstrm and to within a few tenths of a degree, respectively. The atoms in a crystal are also not static, but oscillate about their mean positions, usually by less than a few tenths of an ngstrm. Xray crystallography allows the size of these oscillations to be measured quantitatively.

[edit] Procedure
The technique of single-crystal X-ray crystallography has three basic steps. The first and often most difficult step is to obtain an adequate crystal of the material under study. The crystal should be sufficiently large (typically larger than 100 micrometres in all dimensions), pure in composition and regular in structure, with no significant internal imperfections such as cracks or twinning. A small or irregular crystal will give fewer and less reliable data, from which it may be impossible to determine the atomic arrangement. In the second step, the crystal is placed in an intense beam of X-rays, usually of a single wavelength (monochromatic X-rays), producing the regular pattern of reflections. As the crystal is gradually rotated, previous reflections disappear and new ones appear; the intensity of every spot is recorded at every orientation of the crystal. Multiple data sets may have to be collected, with each set covering slightly more than half a full rotation of the crystal and typically containing tens of thousands of reflection intensities.

In the third step, these data are combined computationally with complementary chemical information to produce and refine a model of the arrangement of atoms within the crystal. The final, refined model of the atomic arrangement now called a crystal structure is usually stored in a public database.

[edit] Limitations
See also: Resolution (electron density) As the crystal's repeating unit, its unit cell, becomes larger and more complex, the atomic-level picture provided by X-ray crystallography becomes less well-resolved (more "fuzzy") for a given number of observed reflections. Two limiting cases of X-ray crystallography"small-molecule" and "macromolecular" crystallographyare often discerned. Small-molecule crystallography typically involves crystals with fewer than 100 atoms in their asymmetric unit; such crystal structures are usually so well resolved that the atoms can be discerned as isolated "blobs" of electron density. By contrast, macromolecular crystallography often involves tens of thousands of atoms in the unit cell. Such crystal structures are generally less well-resolved (more "smeared out"); the atoms and chemical bonds appear as tubes of electron density, rather than as isolated atoms. In general, small molecules are also easier to crystallize than macromolecules; however, X-ray crystallography has proven possible even for viruses with hundreds of thousands of atoms.

X-ray sources
Further information: Diffractometer and Synchrotron The mounted crystal is then irradiated with a beam of monochromatic X-rays. The brightest and most useful X-ray sources are synchrotrons; their much higher luminosity allows for better resolution. They also make it convenient to tune the wavelength of the radiation, which is useful for multi-wavelength anomalous dispersion (MAD) phasing, described below. Synchrotrons are generally national facilities, each with several dedicated beamlines where data is collected around the clock, seven days a week.

A diffractometer Smaller, weaker X-ray sources are often used in laboratories to check the quality of crystals before bringing them to a synchrotron and sometimes to solve a crystal structure. In such systems, electrons are boiled off of a cathode and accelerated through a strong electric potential of roughly 50 kV; having reached a high speed, the electrons collide with a metal plate, emitting bremsstrahlung and some strong spectral lines corresponding to the excitation of inner-shell electrons of the metal. The most common metal used is copper, which can be kept cool easily, due to its high thermal conductivity, and which produces strong K and K lines. The K line is sometimes suppressed with a thin layer (0.0005 in. thick) of nickel foil. The simplest and cheapest variety of sealed X-ray tube has a stationary anode (the Crookes tube) and produces circa 2 kW of X-ray radiation. The more expensive variety has a rotating-anode type source that produces circa 14 kW of X-ray radiation. X-rays are generally filtered to a single wavelength (made monochromatic) and collimated to a single direction before they are allowed to strike the crystal. The filtering not only simplifies the data analysis, but also removes radiation that degrades the crystal without contributing useful information. Collimation is done either with a collimator (basically, a long tube) or with a clever arrangement of gently curved mirrors. Mirror systems are preferred for small crystals (under 0.3 mm) or with large unit cells (over 150 ).

Small-angle X-ray scattering

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(Redirected from Small angle X-ray scattering (SAXS)) Jump to: navigation, search Small-angle X-ray scattering (SAXS) is a small-angle scattering (SAS) technique where the elastic scattering of X-rays (wavelength 0.1 ... 0.2 nm) by a sample which has inhomogeneities in the nm-range, is recorded at very low angles (typically 0.1 - 10). This angular range contains information about the shape and size of macromolecules, characteristic distances of partially ordered materials, pore sizes, and other data. SAXS is capable of delivering structural information of macromolecules between 5 and 25 nm, of repeat distances in partially ordered systems of up to 150 nm.[1] USAXS (ultra-small angle X-ray scattering) can resolve even larger dimensions.

SAXS and USAXS belong to a family of X-ray scattering techniques that are used in the characterization of materials. In the case of biological macromolecules such as proteins, the advantage of SAXS over crystallography is that a crystalline sample is not needed. NMR methods encounter problems with macromolecules of higher molecular mass (> 30000-40000). However, owing to the random orientation of dissolved or partially ordered molecules, the spatial averaging leads to a loss of information in SAXS compared to crystallography.

Applications
SAXS is used for the determination of the microscale or nanoscale structure of particle systems in terms of such parameters as averaged particle sizes, shapes, distribution, and surface-to-volume ratio. The materials can be solid or liquid and they can contain solid, liquid or gaseous domains (so-called particles) of the same or another material in any combination. Not only particles, but also the structure of ordered systems like lamellae, and fractal-like materials can be studied. The method is accurate, non-destructive and usually requires only a minimum of sample preparation. Applications are very broad and include colloids of all types, metals, cement, oil, polymers, plastics, proteins, foods and pharmaceuticals and can be found in research as well as in quality control. The X-ray source can be a laboratory source or synchrotron light which provides a higher X-ray flux.

[edit] SAXS instruments

In a SAXS instrument a monochromatic beam of X-rays is brought to a sample from which some of the X-rays scatter, while most simply go through the sample without interacting with it. The scattered X-rays form a scattering pattern which is then detected at a detector which is typically a 2-dimensional flat X-ray detector situated behind the sample perpendicular to the direction of the primary beam that initially hit the sample. The scattering pattern contains the information on the structure of the sample. The major problem that must be overcome in SAXS instrumentation is the separation of the weak scattered intensity from the strong main beam. The smaller the desired angle, the more difficult this becomes. The problem is comparable to one encountered when trying to observe a weakly radiant object close to the sun, like the sun's corona. Only if the moon blocks out the main light source does the corona become visible. Likewise, in SAXS the non-scattered beam that merely travels through the sample must be blocked, without blocking the closely adjacent scattered radiation. Most available X-ray sources produce divergent beams and this compounds the problem. In principle the problem could be overcome by focusing the beam, but this is not easy when dealing with X-rays

and was previously not done except on synchrotrons where large bent mirrors can be used. This is why most laboratory small angle devices rely on collimation instead. Laboratory SAXS instruments can be divided into two main groups: point-collimation and line-collimation instruments: 1. Point-collimation instruments have pinholes that shape the X-ray beam to a small circular or elliptical spot that illuminates the sample. Thus the scattering is centro-symmetrically distributed around the primary X-ray beam and the scattering pattern in the detection plane consists of circles around the primary beam. Owing to the small illuminated sample volume and the wastefulness of the collimation process only those photons are allowed to pass that happen to fly in the right direction the scattered intensity is small and therefore the measurement time is in the order of hours or days in case of very weak scatterers. If focusing optics like bent mirrors or bent monochromator crystals or collimating and monochromating optics like multilayers are used, measurement time can be greatly reduced. Point-collimation allows to determine the orientation of nonisotropic systems (fibres, sheared liquids). 2. Line-collimation instruments confine the beam only in one dimension so that the beam profile is a long but narrow line. The illuminated sample volume is much larger compared to point-collimation and the scattered intensity at the same flux density is proportionally larger. Thus measuring times with line-collimation SAXS instruments are much shorter compared to point-collimation and are in the range of minutes to hours. This disadvantage is that the recorded pattern is essentially an integrated superposition (a self-convolution) of many pinhole adjacent pinhole patterns. The resulting smearing can be removed using deconvolution methods based on Fourier transformation, but only if the system is isotropic. Line collimation is becoming less and less used in small-angle X-ray scattering due to the increasing number of synchrotron sources which are all point sources, and due to the availability of more powerful X-ray laboratory sources in combination with new multilayer optics.

Wide angle X-ray scattering (WAXS) or Wide angle X-ray diffraction (WAXD) is an X-ray diffraction technique that is often used to determine the crystalline structure of polymers. This technique specifically refers to the analysis of Bragg Peaks scattered to wide angles, which (by Bragg's law) implies that they are caused by sub-nanometer sized structures. Wide angle x-ray scattering is the same technique as Small-Angle X-ray Scattering (SAXS) only the distance from sample to the detector is shorter and thus diffraction maxima at larger angles are observed.

The technique is a time-honored but a somewhat out-of-favor technique for the determination of degree of crystallinity of polymer samples. A diffraction technique for polycrystalline films where only crystallites diffract which are parallel to the substrate surface. The diffraction pattern generated allows to determine the chemical composition or phase composition of the film, the texture of the film (preferred alignment of crystallites), the crystallite size and presence of film stress. According to this method the sample is scanned in a wide angle X-ray goniometer, and the scattering intensity is plotted as a function of the 2 angle. X ray diffraction is a non destructive method of characterization of solid materials. When X-rays are directed in solids they will scatter in predictable patterns based upon the internal structure of the solid. A crystalline solid consists of regularly spaced atoms (electrons) that can be described by imaginary planes. The distance between these planes is called the d-spacing. The intensity of the d-space pattern is directly proportional to the number of electrons (atoms) that are found in the imaginary planes. Every crystalline solid will have a unique pattern of d-spacings (known as the powder pattern), which is a finger print for that solid. In fact solids with the same chemical composition but different phases can be identified by their pattern of dspacings.

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X-ray Crystallography
About the Unit Cell
Crystals are three dimensional ordered structures than can be described as a repetition of identical unit cells. The unit cell is made up of the smallest possible volume that when repeated, is representative of the entire crystal. The dimensions of a unit cell can be described with 3 edge lengths (a,b,c) and 3 angles (alpha, beta, gamma). The 3D location of atoms within a unit cell can be listed as their x, y, z Cartesian Coordinates. Space groups describe the symmetry of a unit cell, of which there are 230 variations. In the molecular origami program, by clicking on Use Crystallographic Info NOW, you can experiment with all the different types of space groups.

Why are X-rays used ?

Using visible light, it will never be possible to see atoms under even the most powerful of microscopes. In order for an object to be seen, its size needs to be at least half the wavelength of the light being used to see it. Since visible light has a wavelength much longer that the distance between atoms it is useless to see molecules. In order to see molecules it is necessary to use a form of electromagnetic radiation with a wavelength on the order of bond lengths, such as X-rays.

Why X-ray diffraction ?

Unfortunately, unlike with visible light, there is no known way to focus x-rays with a lens. This causes an x-ray microscope to be unfeasible unless someone finds a way of focusing x-rays. Until then it is necessary to use crystals to diffract x-rays and create a diffraction pattern which can be interpreted mathematically by a computer. This turns the computer into a virtual lens, so it on a monitor we can look at the structure of a molecule. Crystals are important because by definition they have a repeated unit cell within them. The x-ray diffraction from one unit cell would not be significant. Fortunately, the repetition of unit cells within a crystal amplifies the diffraction enough to give results that computers can turn into a picture.

Growing Crystals
To perform x-ray crystallography, it is necessary to grow crystals with edges around 0.10.3 mm. Crystals are formed as the conditions in a supersaturated solution slowly change. There are three degrees of saturation in solution, and crystallographers take advantage of these when growing crystals: Unsaturated - where no crystals will form or grow. Low supersaturated - where crystals will grow but no new ones will form. High supersaturated - where crystals will both form and grow. One theory of crystal growth is to start by getting a few crystals to grow in the highly supersaturated solution. Then the crystals are exposed to a less saturated solution so they can grow. This is done either by moving the crystals or changing the saturation of the solution. For small molecules, growing large enough crystals is relatively simple. By taking a supersaturated solution of solution and gradually changing the conditions, crystals will begin to grow. If left undisturbed for a few days ideally a few large crystals will grow. Proteins are difficult to crystallize because of their complexity and the fact that protein scientists are usually working with small amounts of protein. There are various methods of growing protein crystals:

Vapor Diffusion -(Hanging Drop Method) This is probably the most common ways of crystal growth. A drop of protein solution is suspended over a reservoir containing buffer and precipitant. Water diffuses from the drop to the solution leaving the drop with optimal crystal growth conditions. Batch crystallization A saturated protein solution left in a sealed container to let the crystals grow. Microbatch crystallization A drop of protein solution is put in inert oil and left to grow. Here there probably is some diffusion of proteins into the oil, lowering the saturation over time. Macroseeding A crystal is grown in a highly saturated solution and placed in a less saturated one where only growth of the crystal will occur. Microseeding A few crystals are grown, then crushed, and put into a final solution that combines them into a few nice crystals. This involves quite a bit of experimentation with solutions' concentrations to get the desired number of crystals. Free interface diffusion A container has levels of varying saturation. Crystals form initially in the highly saturated part, but as the solution mixes, it eventually only supports crystal growth. Dialysis Similar to the previous, but with a semipermeable membrane separating the layers. Proteins are crystallized on such a small scale that it is difficult to reproduce concentrations. This makes crystallizing proteins almost more of an art than a science, and sometimes multiple methods are tried before crystals of the required size are grown.

Applications:

An Introductory Course by Bernhard Rupp What is X-ray Crystallography ?

X-ray crystallography is an experimental technique that exploits the fact that X-rays are diffracted by crystals. It is not an imaging technique. X-rays have the proper wavelength (in the ngstrm range, ~10-8 cm) to be scattered by the electron cloud of an atom of comparable size. Based on the diffraction pattern obtained from X-ray scattering off the periodic assembly of molecules or atoms in the crystal, the electron density can be reconstructed. Additional phase information must be extracted either from the diffraction data or from supplementing diffraction experiments to complete the reconstruction (the phase problem in crystallography). A model is then progressively built into the experimental electron density, refined against the data and the result is a quite accurate molecular structure.

Why Crystallography ?
The knowledge of accurate molecular structures is a prerequisite for rational drug design and for structure based functional studies to aid the development of effective therapeutic agents and drugs. Crystallography can reliably provide the answer to many structure related questions, from global folds to atomic details of bonding. In contrast to NMR, which is an indirect spectroscopic method, no size limitation exists for the molecule or complex to be studied. The price for the high accuracy of crystallographic structures is that a good crystal must be found, and that limited information about the molecule's dynamic behavior in solution is available from one single diffraction experiment. In the core regions of the molecules, X-ray and NMR structures agree very well, and enzymes maintain their activity even in crystals, which often requires the design of non-reactive substrates to study enzyme mechanisms

Application
There is no technique that can match the speed and reliability of single crystal X-ray diffraction for determining the structure of molecules in the solid state. oXray provides industrial customers with fast, reliable, secure access to small molecule crystal structure determination.

Crystals

X-ray diffraction

3D atomic structure

A range of services are available for analysis of crystalline samples: from rapid determination or confirmation of chemical connectivity through to a thorough characterization suitable for publication or patent filings.

Although x-ray crystallography is not new, the application of the technique as part of the effort to determine and analyze the molecular structure of proteins is new. Protein crystallography utilizes single crystal x-ray diffractometry to create three-dimensional models of proteins. This technique has become the focus of structural genomics, which aims to model, examine and analyze protein structures in order to understand disease and design drugs. The long-term, far reaching implications of such research are a new approach to microbiology and proteomics. Along with advances in bioinformatics, automation and digital imaging, advances in crystallography are integral to the development of proteomics. At the moment, this market is in transition as new opportunities are created and explored. X-ray diffraction involves the scattering of a x-ray into several beams when it hits a crystal. By changing the orientation of the crystal, and then measuring and analyzing the angles and intensities of the beams, also known as reflections, the structure of the protein can be modeled using computers to create an electron density map and three-dimensional model. opportunities are created and explored. X-ray diffraction involves the scattering of a x-ray into several beams when it hits a crystal. By changing the orientation of the crystal, and then measuring and analyzing the angles and intensities of the beams, also known as reflections, the structure of the protein can be modeled using computers to create an electron density map and three-dimensional model. Private efforts are also underway as well. Pharmacopeia subsidiary Molecular Simulations, a molecular modeling and simulation software company, recently formed the High Throughput Crystallography Consortium. Members include Abbott Laboratories, Exelixis

and Genencor International. Such a project places Molecular Simulations at the forefront of crystollography development for proteomic applications. The purchase of Emerald Biostructures, a high-throughput protein crystallization company, by Medichem, a discovery chemistry and technology company, is also a sign of the financial promise of such projects. San Diego-based Structural GenomiX is also taking on the project with plans to industrialize the process of protein structure determination. The above efforts, as well as others, signal a new chapter in crystallography in that they represent a systematic approach to the structural determination of genes, which requires multiple partners and the development of enhanced technology. The advent of new methods and the modification of tools for such an approach will lead to faster, more efficient and highly integrated instruments. The new direction of such research, the infusion of money and a collaborative approach will fundamentally change the technology and its applications. Yet larger instrument companies have yet to play a significant role in this market as academic, government research and smaller companies take the initiative. The market leaders in single crystal x-ray diffractometry, Philips Analytical, Rigaku and Bruker AXS, can all expect a growing demand for their x-ray diffractometers, but the full extent of what technology is required and how these companies will fit into this research market has yet to be determined. Of the three companies, it is Rigaku that appears to have the closest ties to the proteomic determination market though its ownership of Molecular Structure Corp., which provides x-ray crystallography services and distributes Rigaku x-ray diffractometers and accesssories. Private efforts are also underway as well. Pharmacopeia subsidiary Molecular Simulations, a molecular modeling and simulation software company, recently formed the High Throughput Crystallography Consortium. Members include Abbott Laboratories, Exelixis and Genencor International. Such a project places Molecular Simulations at the forefront of crystollography development for proteomic applications. The purchase of Emerald Biostructures, a high-throughput protein crystallization company, by Medichem, a discovery chemistry and technology company, is also a sign of the financial promise of such projects. San Diego-based Structural GenomiX is also taking on the project with plans to industrialize the process of protein structure determination.

The above efforts, as well as others, signal a new chapter in crystallography in that they represent a systematic approach to the structural determination of genes, which requires multiple partners and the development of enhanced technology. The advent of new methods and the modification of tools for such an approach will lead to faster, more efficient and highly integrated instruments. The new direction of such research, the infusion of money and a collaborative approach will fundamentally change the technology and its applications. Yet larger instrument companies have yet to play a significant role in this market as academic, government research and smaller companies take the initiative. The market leaders in single crystal x-ray diffractometry, Philips Analytical, Rigaku and Bruker AXS, can all expect a growing demand for their x-ray diffractometers, but the full extent of what technology is required and how these companies will fit into this research market has yet to be determined. Of the three companies, it is Rigaku that appears to have the closest ties to the proteomic determination market though its ownership of Molecular Structure Corp., which provides x-ray crystallography services and distributes Rigaku x-ray diffractometers and accesssories.