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X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles and intensities of these diffracted beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal. From this electron density, the positions of the atoms in the crystal can be determined, as well as their chemical bonds, crystallographic disorder, and various other information.
Extended X-ray absorption fine structure (EXAFS), along with X-ray absorption near edge structure (XANES), is a subset of X-ray absorption spectroscopy (XAS). Like other absorption spectroscopies, XAS techniques follow Beer's law. The X-ray absorption coefficient of a material as a function of energy is obtained by directing X-rays of a narrow energy range at a sample, while recording the incident and transmitted x-ray intensity, as the incident x-ray energy is incremented.
In physics, the phase problem is the problem of loss of information concerning the phase that can occur when making a physical measurement. The name comes from the field of X-ray crystallography, where the phase problem has to be solved for the determination of a structure from diffraction data. The phase problem is also met in the fields of imaging and signal processing. Various approaches of phase retrieval have been developed over the years.
Selenomethionine (SeMet) is a naturally occurring amino acid. The L-selenomethionine enantiomer is the main form of selenium found in Brazil nuts, cereal grains, soybeans, and grassland legumes, while Se-methylselenocysteine, or its γ-glutamyl derivative, is the major form of selenium found in Astragalus, Allium, and Brassica species. In vivo, selenomethionine is randomly incorporated instead of methionine. Selenomethionine is readily oxidized.
Electron crystallography is a method to determine the arrangement of atoms in solids using a transmission electron microscope (TEM). It can involve the use of high-resolution transmission electron microscopy images, electron diffraction patterns including convergent-beam electron diffraction or combinations of these. It has been successful in determining some bulk structures, and also surface structures. Two related methods are low-energy electron diffraction which has solved the structure of many surfaces, and reflection high-energy electron diffraction which is used to monitor surfaces often during growth.
Powder diffraction is a scientific technique using X-ray, neutron, or electron diffraction on powder or microcrystalline samples for structural characterization of materials. An instrument dedicated to performing such powder measurements is called a powder diffractometer.
Bromodeoxyuridine is a synthetic nucleoside analogue with a chemical structure similar to thymidine. BrdU is commonly used to study cell proliferation in living tissues and has been studied as a radiosensitizer and diagnostic tool in people with cancer.
Crystallographic Information File (CIF) is a standard text file format for representing crystallographic information, promulgated by the International Union of Crystallography (IUCr). CIF was developed by the IUCr Working Party on Crystallographic Information in an effort sponsored by the IUCr Commission on Crystallographic Data and the IUCr Commission on Journals. The file format was initially published by Hall, Allen, and Brown and has since been revised, most recently versions 1.1 and 2.0. Full specifications for the format are available at the IUCr website. Many computer programs for molecular viewing are compatible with this format, including Jmol.
Diffraction topography is a imaging technique based on Bragg diffraction. Diffraction topographic images ("topographies") record the intensity profile of a beam of X-rays diffracted by a crystal. A topography thus represents a two-dimensional spatial intensity mapping of reflected X-rays, i.e. the spatial fine structure of a Laue reflection. This intensity mapping reflects the distribution of scattering power inside the crystal; topographs therefore reveal the irregularities in a non-ideal crystal lattice. X-ray diffraction topography is one variant of X-ray imaging, making use of diffraction contrast rather than absorption contrast which is usually used in radiography and computed tomography (CT). Topography is exploited to a lesser extends with neutrons, and has similarities to dark field imaging in the electron microscope community.
Anomalous X-ray scattering is a non-destructive determination technique within X-ray diffraction that makes use of the anomalous dispersion that occurs when a wavelength is selected that is in the vicinity of an absorption edge of one of the constituent elements of the sample. It is used in materials research to study nanometer sized differences in structure.
Isomorphous replacement (IR) is historically the most common approach to solving the phase problem in X-ray crystallography studies of proteins. For protein crystals this method is conducted by soaking the crystal of a sample to be analyzed with a heavy atom solution or co-crystallization with the heavy atom. The addition of the heavy atom (or ion) to the structure should not affect the crystal formation or unit cell dimensions in comparison to its native form, hence, they should be isomorphic.
Single-wavelength anomalous diffraction (SAD) is a technique used in X-ray crystallography that facilitates the determination of the structure of proteins or other biological macromolecules by allowing the solution of the phase problem. In contrast to multi-wavelength anomalous diffraction (MAD), SAD uses a single dataset at a single appropriate wavelength.
A crystallographic database is a database specifically designed to store information about the structure of molecules and crystals. Crystals are solids having, in all three dimensions of space, a regularly repeating arrangement of atoms, ions, or molecules. They are characterized by symmetry, morphology, and directionally dependent physical properties. A crystal structure describes the arrangement of atoms, ions, or molecules in a crystal.
In crystallography, mosaicity is a measure of the spread of crystal plane orientations. A mosaic crystal is an idealized model of an imperfect crystal, imagined to consist of numerous small perfect crystals (crystallites) that are to some extent randomly misoriented. Empirically, mosaicities can be determined by measuring rocking curves. Diffraction by mosaics is described by the Darwin–Hamilton equations.
The Multipole Density Formalism is an X-ray crystallography method of electron density modelling proposed by Niels K. Hansen and Philip Coppens in 1978. Unlike the commonly used Independent Atom Model, the Hansen-Coppens Formalism presents an aspherical approach, allowing one to model the electron distribution around a nucleus separately in different directions and therefore describe numerous chemical features of a molecule inside the unit cell of an examined crystal in detail.
In crystallography, direct methods is a set of techniques used for structure determination using diffraction data and a priori information. It is a solution to the crystallographic phase problem, where phase information is lost during a diffraction measurement. Direct methods provides a method of estimating the phase information by establishing statistical relationships between the recorded amplitude information and phases of strong reflections.
Quantum crystallography is a branch of crystallography that investigates crystalline materials within the framework of quantum mechanics, with analysis and representation, in position or in momentum space, of quantities like wave function, electron charge and spin density, density matrices and all properties related to them. Like the quantum chemistry, Quantum crystallography involves both experimental and computational work. The theoretical part of quantum crystallography is based on quantum mechanical calculations of atomic/molecular/crystal wave functions, density matrices or density models, used to simulate the electronic structure of a crystalline material. While in quantum chemistry, the experimental works mainly rely on spectroscopy, in quantum crystallography the scattering techniques play the central role, although spectroscopy as well as atomic microscopy are also sources of information.
Serial femtosecond crystallography (SFX) is a form of X-ray crystallography developed for use at X-ray free-electron lasers (XFELs). Single pulses at free-electron lasers are bright enough to generate resolvable Bragg diffraction from sub-micron crystals. However, these pulses also destroy the crystals, meaning that a full data set involves collecting diffraction from many crystals. This method of data collection is referred to as serial, referencing a row of crystals streaming across the X-ray beam, one at a time.
Lieselotte Templeton was a German-born American crystallographer. She received the Patterson Award of the American Crystallographic Association together with her husband David H. Templeton in 1987.
This is a timeline of crystallography.
References
- ↑ Hendrickson W, Ogata C (1997). Phase determination from multiwavelength anomalous diffraction measurements. Methods in Enzymology. Vol. 276. pp. 494–523. doi:10.1016/S0076-6879(97)76074-9. ISBN 978-0-12-182177-7. PMID 27799111.
- ↑ Hendrickson WA (1985). "Analysis of Protein Structure from Diffraction Measurement at Multiple Wavelengths". Transactions of the ACA. 21.
- ↑ "Dictionary of common terms used in PHENIX". phenix-online.org.
MAD: [...] The differences in anomalous scattering around the edge allow calculation of phase angles without the phase ambiguity present in SAD experiments, although density modification will usually still be necessary to obtain an easily interpretable map. [...] Although very powerful, MAD phasing has declined somewhat in popularity relative to SAD because of the more limited choice of heavy atoms, the difficulty of avoiding radiation damage, and the requirement for a synchrotron beamline.
Further reading
- Hendrickson WA (1985). "Analysis of Protein Structure from Diffraction Measurement at Multiple Wavelengths". Transactions of the ACA. 21.
- Karle J (1980). "Some Developments in Anomalous Dispersion for the Structural Investigation of Macromolecular Systems in Biology". International Journal of Quantum Chemistry: Quantum Biology Symposium. 7: 357–367. doi:10.1002/qua.560180734.
- Karle J (1989). "Linear Algebraic Analyses of Structures with One Predominant Type of Anomalous Scatterer". Acta Crystallographica A. 45 (4): 303–307. doi:10.1107/s0108767388013042. PMID 2559755.
- Pahler A, Smith JL, Hendrickson WA (1990). "A Probability Representation for Phase Information from Multiwavelength Anomalous Dispersion". Acta Crystallographica A. 46 (7): 537–540. doi:10.1107/s0108767390002379. PMID 2206480.
- Terwilliger TC (1994). "MAD Phasing: Bayesian Estimates of FA". Acta Crystallographica D. 50 (Pt 1): 11–16. doi: 10.1107/s0907444993008224 . PMID 15299471.
- Terwilliger TC (1994). "MAD Phasing: Treatment of Dispersive Differences as Isomorphous Replacement Information". Acta Crystallographica D. 50 (Pt 1): 17–23. doi: 10.1107/s0907444993008236 . PMID 15299472.
- Fourme R, Shepard W, Kahn R, l'Hermite G, de La Sierra IL (1995). "The Multiwavelength Anomalous Solvent Contrast (MASC) Method in Macrocolecular Crystallography". Journal of Synchrotron Radiation. 2 (Pt 1): 36–48. doi: 10.1107/S0909049594006680 . PMID 16714785.
- de la Fortelle E, Bricogne G (1997). Maximum-Likelihood Heavy-Atom Parameter Refinement for Multiple Isomorphous Replacement and Multiwavelength Anomalous Diffraction Methods. Methods in Enzymology. Vol. 276. pp. 472–494. doi:10.1016/S0076-6879(97)76073-7. ISBN 978-0-12-182177-7. PMID 27799110.
- Hendrickson WA, Ogata CM (1997). Phase Determination from Multiwavelength Anomalous Diffraction Measurements. Methods in Enzymology. Vol. 276. pp. 494–523. doi:10.1016/S0076-6879(97)76074-9. ISBN 978-0-12-182177-7. PMID 27799111.
- Bella J, Rossmann MG (1998). "A General Phasing Algorithm for Multiple MAD and MIR Data". Acta Crystallographica D. 54 (2): 159–174. doi:10.1107/s0907444997010469. PMID 9761882.
- Guss JM, Merritt EA, Phizackerley RP, Hedman B, Murata M, Hodgson KO, Freeman HC (1989). "Phase determination by multiple-wavelength X-ray diffraction: crystal structure of a basic blue copper protein from cucumbers". Science. 241 (4867): 806–811. Bibcode:1988Sci...241..806G. doi:10.1126/science.3406739. PMID 3406739.