Using the parallel tempering algorithm to overcome complex problems in structure determination of inorganic materials with laboratory X-rays

2006 ◽  
Vol 2006 (suppl_23_2006) ◽  
pp. 9-14 ◽  
Author(s):  
T. Bataille ◽  
N. Mahé ◽  
E. Le Fur ◽  
J.-Y. Pivan ◽  
D. Louer
IUCrJ ◽  
2017 ◽  
Vol 4 (5) ◽  
pp. 639-647 ◽  
Author(s):  
Keitaro Yamashita ◽  
Naoyuki Kuwabara ◽  
Takanori Nakane ◽  
Tomohiro Murai ◽  
Eiichi Mizohata ◽  
...  

Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) holds enormous potential for the structure determination of proteins for which it is difficult to produce large and high-quality crystals. SFX has been applied to various systems, but rarely to proteins that have previously unknown structures. Consequently, the majority of previously obtained SFX structures have been solved by the molecular replacement method. To facilitate protein structure determination by SFX, it is essential to establish phasing methods that work efficiently for SFX. Here, selenomethionine derivatization and mercury soaking have been investigated for SFX experiments using the high-energy XFEL at the SPring-8 Angstrom Compact Free-Electron Laser (SACLA), Hyogo, Japan. Three successful cases are reported of single-wavelength anomalous diffraction (SAD) phasing using X-rays of less than 1 Å wavelength with reasonable numbers of diffraction patterns (13 000, 60 000 and 11 000). It is demonstrated that the combination of high-energy X-rays from an XFEL and commonly used heavy-atom incorporation techniques will enable routinede novostructural determination of biomacromolecules.


Author(s):  
J N Chapman ◽  
W A P Nicholson

Energy dispersive x-ray microanalysis (EDX) is widely used for the quantitative determination of local composition in thin film specimens. Extraction of quantitative data is usually accomplished by relating the ratio of the number of atoms of two species A and B in the volume excited by the electron beam (nA/nB) to the corresponding ratio of detected characteristic photons (NA/NB) through the use of a k-factor. This leads to an expression of the form nA/nB = kAB NA/NB where kAB is a measure of the relative efficiency with which x-rays are generated and detected from the two species.Errors in thin film x-ray quantification can arise from uncertainties in both NA/NB and kAB. In addition to the inevitable statistical errors, particularly severe problems arise in accurately determining the former if (i) mass loss occurs during spectrum acquisition so that the composition changes as irradiation proceeds, (ii) the characteristic peak from one of the minority components of interest is overlapped by the much larger peak from a majority component, (iii) the measured ratio varies significantly with specimen thickness as a result of electron channeling, or (iv) varying absorption corrections are required due to photons generated at different points having to traverse different path lengths through specimens of irregular and unknown topography on their way to the detector.


Author(s):  
K. Chowdhury ◽  
S. Ghosh ◽  
M. Mukherjee

AbstractThe direct method program SAYTAN has been applied successfully to redetermine the structure of cytochrome c


Author(s):  
Frank Marshall ◽  
G. Grubbs II ◽  
Gamil Guirgis ◽  
Theodore Carrigan-Broda ◽  
Grier Jones ◽  
...  

2018 ◽  
Vol 20 (5) ◽  
pp. 411-418 ◽  
Author(s):  
Bernadett Kovacs ◽  
Zoltán Béni ◽  
Miklós Dékány ◽  
Noémi Bózsity ◽  
Istvan Zupko ◽  
...  

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