‘Atomic resolution’: a badly abused term in structural biology

Abstract

The term ‘atomic resolution’ is very often abused in presenting macromolecular structures.

The term ‘atomic resolution’ was defined a long time ago and it is generally accepted to correspond to an electron-density map (or a map calculated using another type of data, for example nuclear density) in which individual atoms can be distinguished. It is usually assumed to correspond to a resolution d _min of 1.2 Å of the diffraction data, which is also known as the ‘Sheldrick criterion’ (Sheldrick, 1990 ▸; Morris & Bricogne, 2003 ▸). This limit is not arbitrary, since it reflects the ability to visualize separated atoms and serves as the basis for the determination of crystal structures by direct methods, but it might of course be adjusted if valid scientific reasons could be presented. The meaning of ‘near-atomic resolution’ is much more diffuse, but in our opinion it should be restricted to d _min < 2 Å, the resolution at which the backbone atoms of a protein chain can be assigned with a high degree of confidence. However, these terms are very often abused in order for the published structures to appear to be more accurate than they are in reality. Thus, many X-ray and neutron crystal structures claim ‘atomic resolution’ although they were determined on the basis of data extending to only ∼2 Å or less (Henderson et al., 2011 ▸; Taylor et al., 2011 ▸; Lyu et al., 2014 ▸; Miwa et al., 2016 ▸; Hong et al., 2016 ▸). This term is also sometimes used for structures determined by NMR, in which case the meaning of ‘resolution’ is even more uncertain (Wälti et al., 2016 ▸). More recently, the term ‘near-atomic resolution’ has been used to describe cryo-EM structures determined at resolutions as low as 3.2–4.2 Å (Worrall et al., 2016 ▸; Galkin et al., 2015 ▸; Bartesaghi et al., 2014 ▸; Chua et al., 2016 ▸; von der Ecken et al., 2016 ▸) or an XFEL structure at 3.3 Å resolution (Zhou et al., 2016 ▸). On the other hand, the term ‘near-atomic resolution’ is sometimes used to describe structures at the resolution as high as 1.0 Å (Romir et al., 2007 ▸). Since these terms are currently being used by scientists practicing different techniques for structure determination, an agreement on their exact meanings might be very helpful. In our opinion, the term ‘a structure at atomic resolution’ should not mean ‘a structure represented by individual atoms’, which can be constructed even at low data and map resolution from the known building blocks consisting of separate atoms. We would like to postulate that maybe all structural communities, including traditional macromolecular X-ray and neutron crystallography, XFEL and cryo-EM, among others, should adopt, or indeed respect, standard definitions of what these terms are supposed to mean. Such an agreement would help the readers of structural papers to obtain a realistic impression of the likely accuracy of the structures based on the resolution of the primary experimental data.