Ab initio phase determination for X-ray diffraction data from crystals of a native protein. 1991

L Sjölin, and E Prince, and L A Svensson, and G L Gilliland
Institute for Inorganic Chemistry, Chalmers University of Technology, Göteborg, Sweden.

An efficient algorithm for the determination of an everywhere positive electron-density distribution that agrees with observed structure amplitudes has been used to determine the phases of X-ray diffraction data from recombinant bovine chymosin, a protein with 323 amino-acid residues in the molecular chain whose structure was recently determined using molecular replacement methods. A systematic procedure for testing the signs of centric reflections, using the total entropy of the map as a figure of merit, was used to produce a low-resolution map. The phases of acentric and additional centric reflections were then chosen by adding them to the map with various possible phases and computing the total entropy of the resulting map. Of 159 centric reflections whose phases were chosen by this procedure, 141 had the same phase as in the refined structure. The median absolute phase difference for 1811 acentric reflections was 32 degrees. A map produced from these 1970 reflections, out of 12,346 reflections in the data set, showed a remarkable agreement with the refined structure. This molecule is many times larger than any whose structures have previously been determined without the use of isomorphous replacement, molecular replacement or anomalous dispersion, and the map demonstrates the potential of maximum-entropy methods in macromolecular structure determination.

UI MeSH Term Description Entries
D008433 Mathematics The deductive study of shape, quantity, and dependence. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed) Mathematic
D008956 Models, Chemical Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment. Chemical Models,Chemical Model,Model, Chemical
D012085 Chymosin The predominant milk-clotting enzyme from the true stomach or abomasum of the suckling calf. It is secreted as an inactive precursor called prorennin and converted in the acid environment of the stomach to the active enzyme. EC 3.4.23.4. Rennin,Chymosin A,Chymosin C
D005583 Fourier Analysis Analysis based on the mathematical function first formulated by Jean-Baptiste-Joseph Fourier in 1807. The function, known as the Fourier transform, describes the sinusoidal pattern of any fluctuating pattern in the physical world in terms of its amplitude and its phase. It has broad applications in biomedicine, e.g., analysis of the x-ray crystallography data pivotal in identifying the double helical nature of DNA and in analysis of other molecules, including viruses, and the modified back-projection algorithm universally used in computerized tomography imaging, etc. (From Segen, The Dictionary of Modern Medicine, 1992) Fourier Series,Fourier Transform,Analysis, Cyclic,Analysis, Fourier,Cyclic Analysis,Analyses, Cyclic,Cyclic Analyses,Series, Fourier,Transform, Fourier
D000465 Algorithms A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task. Algorithm
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D013816 Thermodynamics A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed) Thermodynamic
D014961 X-Ray Diffraction The scattering of x-rays by matter, especially crystals, with accompanying variation in intensity due to interference effects. Analysis of the crystal structure of materials is performed by passing x-rays through them and registering the diffraction image of the rays (CRYSTALLOGRAPHY, X-RAY). (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed) Xray Diffraction,Diffraction, X-Ray,Diffraction, Xray,Diffractions, X-Ray,Diffractions, Xray,X Ray Diffraction,X-Ray Diffractions,Xray Diffractions

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