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Journal of Electron Microscopy Advance Access originally published online on October 17, 2007
Journal of Electron Microscopy 2007 56(4):131-140; doi:10.1093/jmicro/dfm019
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© The Author 2007. Published by Oxford University Press on behalf of Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Simulation of charge effects on density maps obtained by high-resolution electron crystallography

Teruhisa Hirai1,3,*, Kaoru Mitsuoka1,4, Akinori Kidera2,5 and Yoshinori Fujiyoshi1

1 Department of Biophysics, Faculty of Science, Kyoto University, Oiwake, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
2 Department of Chemistry, Faculty of Science, Kyoto University, Oiwake, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan

* To whom correspondence should be addressed. E-mail: thirai{at}spring8.or.jp

Atomic scattering factors for electrons are strongly affected by the charge status of the scattering atoms. The difference in scattering factors for charged and neutral atoms is most pronounced in the resolution range below 5 Å. As a result of the negative scattering factors of negatively charged atoms in the low-resolution range, charged glutamate or aspartate residues produce weaker densities in electron crystallographic maps than their neutral forms. Such charge effects were indeed observed in an experimental map of bacteriorhodopsin. Here we present mathematical simulations of this charge effect on electron crystallographic density maps that corroborate the experimental results. For the simulations, we first evaluated the errors introduced by approximating atomic scattering factors for neutral and charged atoms by Gaussians. The simulations then showed that the effect of a polarized pair of oxygen and hydrogen atoms on the density (polarization effect) was much smaller than that expected from the individual charged atoms (charge effect), due to charge compensation. Still, density maps obtained by electron crystallography are expected to show slightly elongated features toward the positively charged atoms.

Keywords     electron crystallography, scattering factor, density map, charge effect, polarization effect, bacteriorhodopsin

Received     26 February 2007, accepted 21 July 2007

3 Present address: Structural Physiology Research Group, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo, Hyogo 679-5148, Japan

4 Present address: Japan Biological Information Research Center (JBIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan

5 Present address: Graduate School of Integrated Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan


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