Structure Determination by X-Ray Crystallography

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Nowadays X-ray crystallography is used in many fields of chemistry, mineralogy and physics. Not only in the so-called crystalline state ordered position of ions, atoms or molecules but also in the amorphous and liquid states that do not have long-order periodicity. Crystallographic analysis needs the highest quality diffraction data. Product range. Product category.


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Crystallographic analysis of X-ray diffraction data. The ancient Greeks believed that Krystallos crystal was light frozen into ice and that it was so hard that it could never be melted. In later times, crystallography started as a science which studied the outer symmetry of crystals in order to try to explain the inner side of crystals. Father and son Bragg were the first ones that used X-ray diffraction XRD to study the inside of crystals and showed the periodic arrangement of atoms in a crystal. Contact sales Register now.

Protein structure determination by x-ray crystallography.

Empyrean range. Previous reflections disappear and new ones appear along with the gradual rotation of the crystal, and the intensity of every spot is recorded at every orientation of the crystal. Multiple data sets may have to be collected since each set covers slightly more than half a full rotation of the crystal and typically contains tens of thousands of reflections. Ultimately, these collected data are combined computationally with complementary chemical information to obtain and refine a model from the arrangement of atoms within the crystal.


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The final refined model of the atomic arrangement is called a crystal structure and usually stored in a public database. Figure 1. Workflow for solving the molecular structure by X-ray crystallography. In most cases, the generation of a diffraction-quality crystal is a primary barrier to solve its atomic-resolution structure.

A pure crystal of high regularity is a general requirement in crystallography to solve the structure of a complicated arrangement of atoms. There are many methods to cultivate crystal, such as gas diffusion, liquid phase diffusion, temperature gradient, vacuum sublimation, convection and so on, and the most widely adopted methodology is gas phase diffusion, which can be further divided into hanging drop, sitting drop, oil drop and microdialysis.

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The crystallography of small molecules and macromolecular differs in the range of possible techniques applied to produce diffraction-quality crystals. Small molecules have few degrees of conformational freedom, and can be crystallized by a wide range of methods. On the contrary, macromolecules have too many degrees of freedom to achieve a perfect crystallization so as to maintain a stable structure.

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The range of crystallization conditions is also restricted to solution conditions where biomacromolecules remain folded configuration. There are several factors known to inhibit or ruin crystallization. Crystals generally grow at a constant temperature and are protected from shocks or vibrations that possibly disturb the crystallization.

Impurities in the molecules or crystallization solutions are also inimical to crystallization. Molecules with high conformational flexibility or high tendcency to self-assemble into regular helices are often unwilling to assemble into crystals.


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A slight change in molecular properties can even lead to large differences in crystallization behavior. After acquiring the initial conditions of crystal growth, it is often necessary to optimize the crystallization conditions by adjusting precipitant concentration, pH value, sample concentration, temperature and ionic strength.

Figure 2. Diffraction experiments are needed after obtaining single crystal.

The X-ray irradiating to the crystal is diffracted, and the diffraction data are recorded. X-ray has are two main sources, one of which applied in the common X-ray instrument produces X-rays with multiple characteristic wavelengths by bombarding copper targets or molybdenum targets with high energy electron flow. Another one is the X-ray with variable wavelength generated through synchrotron radiation.

The experimental principle of ADXD is the same as that of the normal X-ray diffractometer, while the wavelength is lower and the energy is higher. The incident light of EDXRD is white light with a continuous wavelength, and the diffraction signal is collected at a fixed angle. Diffraction data, including location and intensity of diffraction points, are often recorded by image plates or CCD detectors. The analysis of the recorded diffraction data could indicate the corresponding crystal system and Bravais lattice of crystal, and reveal the miller index and intensity of each diffraction point in the inverted space.

Frist of all, indexation, strength integration, consolidation, and amplitude reduction are executed in data analysis procedure. Some problems in the determination of crystallographic parameters are then discussed, which is followed by common data collection and program processing. The intensity data of crystal diffraction finally undergoes a quality assessment. Each recorded series of two-dimensional diffraction patterns corresponding to a different crystal orientation, is converted into a three-dimensional model of the electron density, which is completed by the mathematical technique of Fourier transforms.

Each spot has a corresponding type of variation in the electron density and which variation corresponds to which spot indexing must be determined.

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The relative strengths of the spots in different images merging and scaling and how the variations should be combined to yield the total electron density phasing are also necessary to be figured out. Data processing commences with the reflections indexation, which means identifying the dimensions of the unit cells and which image peak stands for which position in reciprocal space.

A byproduct of indexing is to determine the crystal symmetry. The data is then integrated after having assigned symmetry. The hundreds of images containing the thousands of reflections are converted into a single file that consists of records of the miller index of each reflection and intensity for each reflection. These various images taken at different orientations of the crystal are merged and scaled firstly to identify which peaks appear in two or more images merging and to scale the relative images so that they have a consistent intensity scale. The optimization of intensity scale is critical for the peaks intensity since they are the key information from which the structure is determined.

The repetitive technique of crystallographic data collection and the high symmetry of crystalline materials lead the diffractometer to repeatedly record many symmetry-equivalent reflections, allowing the calculation of symmetry-related R -factor, which is a reliable index based upon how similar are the measured intensities of symmetry-equivalent reflections, thus evaluating the quality of the data. The data collected from a diffraction experiment represents a reciprocal space of the crystal lattice.

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