CHOOCH: a program for deriving anomalous-scattering factors from X-ray fluorescence spectra

2001 ◽  
Vol 34 (1) ◽  
pp. 82-86 ◽  
Author(s):  
Gwyndaf Evans ◽  
Robert F. Pettifer
Keyword(s):  
Absorption Edge ◽  
Fluorescence Spectra ◽  
Heavy Atom ◽  
Fortran Program ◽  
Anomalous Scattering ◽  
Tabular Data ◽  
X Ray ◽  
Scattering Factor ◽  
Experimental Values ◽  
Kronig Relation

A Fortran programCHOOCH, which derives experimental values of the anomalous-scattering factorsf′′ andf′ from X-ray fluorescence spectra, is described. The program assumes knowledge of theoretical values for the imaginary term,f′′, of the anomalous-scattering factor away from the absorption edge to scale the experimental fluorescence spectrum and thus derive values off′′ near the absorption edge, where tabular data are inappropriate. The Kramers–Kronig relation is used to calculate the real part,f′, of the anomalous-scattering factor. The program aids the decision-making process in macromolecular crystallographic experiments where optimal wavelength selection is required. Magnitudes off′ andf′′ at selected wavelengths can later be used as starting values for heavy-atom refinement with crystallographic phasing programs.

The information available from anomalous scattering on fibres at different wavelengths

1987 ◽  
Vol 20 (4) ◽  
pp. 295-299 ◽  
Author(s):  
C. Nave
Keyword(s):  
Absorption Edge ◽  
Heavy Atom ◽  
Imaginary Component ◽  
Anomalous Scattering ◽  
Phase Problem ◽  
Phase Information ◽  
Helical Symmetry ◽  
X Ray ◽  
The Real ◽  
X Ray Scattering

The contribution of a particular atom in a molecule to the total X-ray scattering can be altered by varying the wavelength in the region of the absorption edge of the atom. It is shown that only the changes in the real part of the anomalous scattering of the atom provide significant changes in a pattern from a fibre containing molecules with helical symmetry. Changes due to the imaginary component are small and Friedel differences cannot be observed, owing to the fibre disorder. The information which can be obtained is equivalent to that given by a truly isomorphous heavy-atom derivative. For the general case this is not sufficient to provide unambiguous phase information. If a twofold axis is present at right angles to the fibre axis then the amplitudes are real and the phase problem can, in favourable cases, be solved.

scholarly journals Alternative phasing method in macromolecular crystallography

2014 ◽  
Vol 70 (a1) ◽  
pp. C342-C342
Author(s):  
Santosh Panjikar ◽  
Daniele de Sanctis
Keyword(s):  
Crystal Structures ◽  
Uv Radiation ◽  
Absorption Edge ◽  
Heavy Atom ◽  
Anomalous Scattering ◽  
Covalent Bonds ◽  
X Ray ◽  
Isomorphous Replacement ◽  
Experimental Phasing ◽  
Radiation Induced

Selenium is the most widely used heavy atom for experimental phasing, either by single anomalous scattering (SAD) or multiple-wavelength anomalous diffraction (MAD) procedures. The use of the single isomorphous replacement (SIR) or single isomorphous replacement with anomalous scattering (SIRAS) phasing procedure with selenomethionine (Mse) containing proteins is not so commonly used, as it requires isomorphous native data. Several non-redundant X-ray diffraction data sets from various Mse derivatised protein crystals were collected at energies far below the absorption edge before and after exposing the crystal to ultraviolet (UV) radiation with 266 nm lasers. A detailed analysis revealed that significant changes in diffracted intensities were induced by ultraviolet irradiation whilst retaining crystal isomorphism. These intensity changes allowed the crystal structures to be solved by the radiation damage-induced phasing (RIP) technique [1]. These can be coupled with the anomalous signal from the dataset collected at the selenium absorption edge to obtain SIRAS phases in a UV-RIPAS phasing experiment [2]. Inspection of the crystal structures and electron-density maps demonstrated that covalent bonds between selenium and carbon at all sites located in the core of the proteins or in a hydrophobic environment were much more susceptible to UV radiation-induced cleavage than other bonds typically present in Mse proteins. The rapid UV radiation-induced bond cleavage opens a reliable new paradigm for phasing at synchrotron [1,2] and at in-house X-ray source [3].

Determination of the Anomalous Scattering Factors in the Soft-X-ray Range using Diffraction from a Multilayer

1998 ◽  
Vol 31 (5) ◽  
pp. 700-707 ◽  
Author(s):  
L. Sève ◽  
J. M. Tonnerre ◽  
D. Raoux
Keyword(s):  
Fluorescence Yield ◽  
Bragg Diffraction ◽  
Anomalous Scattering ◽  
Total Electron Yield ◽  
Total Electron ◽  
X Ray ◽  
Scattering Factor ◽  
X Ray Absorption ◽  
Kronig Relation

Bragg diffraction from an Ag/Ni multilayer was used to determine independently both the real and imaginary parts of the anomalous scattering factor (ASF) around the NiLIIIandLIIedges in the soft-X-ray range. Huge resonant variations were observed with f'' reaching 55\,r_o and f' decreasing to −63 r_o at the NiLIIIedge. The independent measurements of f' and f'' are tested for coherency using the Kramers–Kronig relation. The f'' values are also compared with those derived from X-ray absorption methods such as total electron yield and fluorescence yield measurements.

A Rietveld-analysis program for X-ray powder spectro-diffractometry

1999 ◽  
Vol 14 (2) ◽  
pp. 106-110 ◽  
Author(s):  
Yanan Xiao ◽  
Shinjiro Hayakawa ◽  
Yohichi Gohshi ◽  
Masaharu Oshima ◽  
Fujio Izumi ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Absorption Edge ◽  
Rietveld Method ◽  
Rietveld Analysis ◽  
Anomalous Scattering ◽  
Analysis Program ◽  
X Ray ◽  
Diffraction Patterns ◽  
X Ray Absorption

In order to exploit X-ray powder spectro-diffractometry, the program RIETAN-97ß for refining crystal structure and lattice parameters by the Rietveld method was modified extensively. The resulting software can be used to refine anomalous scattering factors, fr and fi, for specified crystallographic sites near the X-ray absorption edge of a particular element. The effectiveness of the modified software was tested by using powder diffraction patterns simulated by the original RIETAN-97ß software and a series of measured powder diffraction patterns of Fe3O4 with incident X-ray energies near the absorption edge of iron.

Valence-contrast studies by resonant diffraction with synchrotron radiation; the rôle of X-ray absorption measurements

1992 ◽  
Vol 25 (5) ◽  
pp. 654-657 ◽  
Author(s):  
A. P. Wilkinson ◽  
A. K. Cheetham
Keyword(s):  
Optical Theorem ◽  
Anomalous Scattering ◽  
X Rays ◽  
Acta Cryst ◽  
X Ray ◽  
X Ray Absorption ◽  
Kronig Relation ◽  
Absorption Measurements ◽  
Good Agreement

The X-ray absorption spectra of GaCl2, GaAlCl4 and GaCl3 have been measured in the vicinity of the Ga K edge and values of f′′ and f′ estimated for GaI and GaIII from the latter two spectra by using the optical theorem and the Kramers–Kronig relation. The resulting f′ values are compared with those previously determined from anomalous-scattering measurements with synchrotron X-rays on the compound GaCl2 [Wilkinson, Cheetham & Cox (1991). Acta Cryst. B47, 155–161] and found to be in good agreement. The use of anomalous scattering methods for distinguishing oxidation states is discussed in the light of these results and others found in the literature.

Determination of Anomalous Scattering Factor by Using Transmitted Rocking Curves near the Absorption Edge

1997 ◽  
Vol 36 (Part 1, No. 10) ◽  
pp. 6424-6425 ◽  
Author(s):  
Shengming Zhou ◽  
Masami Yoshizawa ◽  
Tomoe Fukamachi ◽  
Riichiro Negishi ◽  
Takaaki Kawamura ◽  
...  
Keyword(s):  
Absorption Edge ◽  
Anomalous Scattering ◽  
Scattering Factor

Ordered Structure in Lead Magnoniobate (PMN) by Resonant X-Ray Scattering

1996 ◽  
Vol 437 ◽  
Author(s):  
V. Gosula ◽  
Haydn Chen ◽  
S. Teslic ◽  
T. Egami ◽  
S. Vakhrushev
Keyword(s):  
Electron Diffraction ◽  
Absorption Edge ◽  
Relaxor Ferroelectric ◽  
Ordered Structure ◽  
Two Phase ◽  
X Ray ◽  
X Ray Scattering ◽  
Scattering Factor ◽  
Microscopic Origin ◽  
Ray Scattering

AbstractHalf integer superlattice reflections characteristic of ordered structure in PMN (Pb(Mg1,3Nb2,3)O3) single crystal have been measured using resonant synchrotron x-ray scattering near the Pb LIII absorption edge. These superlattice peaks have been previously reported in PMN by electron diffraction, and were interpreted in the context of a two phase Nb/Mg ordering model to explain its relaxor ferroelectric behavior. Nevertheless, the microscopic origin of the superlattice peaks is controversial. Previous results have shown that the Nb atom contributes heavily to the superlattice peaks. However, the effective scattering factor for these peaks is significantly smaller than in the case of complete ordering. In addition, there is strong evidence that lead participates in the ordering.

X-ray determination of polarity sense by anomalous scattering at an absorption edge

1970 ◽  
Vol 3 (1) ◽  
pp. 27-32 ◽  
Author(s):  
R. L. Barns ◽  
E. T. Keve ◽  
S. C. Abrahams
Keyword(s):  
Absorption Edge ◽  
Anomalous Scattering ◽  
X Ray

scholarly journals Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent

2016 ◽  
Vol 113 (46) ◽  
pp. 13039-13044 ◽  
Author(s):  
Takanori Nakane ◽  
Shinya Hanashima ◽  
Mamoru Suzuki ◽  
Haruka Saiki ◽  
Taichi Hayashi ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Structure Determination ◽  
Free Electron ◽  
Heavy Atom ◽  
Anomalous Scattering ◽  
X Ray ◽  
Isomorphous Replacement ◽  
Experimental Phasing ◽  
Serial Femtosecond Crystallography

The 3D structure determination of biological macromolecules by X-ray crystallography suffers from a phase problem: to perform Fourier transformation to calculate real space density maps, both intensities and phases of structure factors are necessary; however, measured diffraction patterns give only intensities. Although serial femtosecond crystallography (SFX) using X-ray free electron lasers (XFELs) has been steadily developed since 2009, experimental phasing still remains challenging. Here, using 7.0-keV (1.771 Å) X-ray pulses from the SPring-8 Angstrom Compact Free Electron Laser (SACLA), iodine single-wavelength anomalous diffraction (SAD), single isomorphous replacement (SIR), and single isomorphous replacement with anomalous scattering (SIRAS) phasing were performed in an SFX regime for a model membrane protein bacteriorhodopsin (bR). The crystals grown in bicelles were derivatized with an iodine-labeled detergent heavy-atom additive 13a (HAD13a), which contains the magic triangle, I3C head group with three iodine atoms. The alkyl tail was essential for binding of the detergent to the surface of bR. Strong anomalous and isomorphous difference signals from HAD13a enabled successful phasing using reflections up to 2.1-Å resolution from only 3,000 and 4,000 indexed images from native and derivative crystals, respectively. When more images were merged, structure solution was possible with data truncated at 3.3-Å resolution, which is the lowest resolution among the reported cases of SFX phasing. Moreover, preliminary SFX experiment showed that HAD13a successfully derivatized the G protein-coupled A2a adenosine receptor crystallized in lipidic cubic phases. These results pave the way for de novo structure determination of membrane proteins, which often diffract poorly, even with the brightest XFEL beams.

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