News

Identification of ions in experimental electrostatic potential maps.
Jimin Wang, Zheng Liu, Joachim Frank and Peter Moore.

International Union of Crystallography Journal

ABSTRACT
Cryo-electron microscopy (EM) directly images the distribution of electrostatic potential
within macromolecules, and thus can provide much more information about atomic
charges than X-ray crystallography normally does. The electron scattering length of an
isolated ion is quite different from that of the corresponding neutral atom. The difference
is very large at small scattering angles where the effects of electron distributions are the
largest, but becomes smaller at high scattering angle where nuclear charge determines
outcomes. For this reason, in cryo-EM maps that have been solved at resolutions lower
than ~ 2.5 Å, peaks that correspond to anions will always be less prominent than those
that correspond to cations, and may even be negative. Furthermore, if a map of this kind
is smeared computationally after the fact, which reduces its effective resolution, anion
peaks will diminish in size, cation peaks will grow, and peaks that represent uncharged
atoms will remain about the same. These effects can be used to determine the sign of the
charges carried by the ions associated with a macromolecule, and even to estimate their
magnitudes. ESP value for a cation in a cation-anion pair is smaller than the value of the
cation in isolation, but ESP value for the anion in the ionic pair is greater than the value
of the anion in isolation. The experimental range of ESP value for Mg2+ relative to that of
the closest C1’ atom are found to be between 0.57 and 1.27.