letters to the editor\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoSTRUCTURAL
BIOLOGY
ISSN: 2059-7983
RESPONSE

A response to this article has been published. To view the response, click here.

`Atomic resolution': a badly abused term in structural biology

aMacromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
*Correspondence e-mail: wlodawer@nih.gov

Edited by J. L. Martin, Griffith University, Australia (Received 22 December 2016; accepted 9 February 2017; online 31 March 2017)

Keywords: atomic resolution.

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 dmin of 1.2 Å of the diffraction data, which is also known as the `Sheldrick criterion' (Sheldrick, 1990[Sheldrick, G. M. (1990). Acta Cryst. A46, 467-473.]; Morris & Bricogne, 2003[Morris, R. J. & Bricogne, G. (2003). Acta Cryst. D59, 615-617.]). 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 dmin < 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[Henderson, J. N., Kuriata, A. M., Fromme, R., Salvucci, M. E. & Wachter, R. M. (2011). J. Biol. Chem. 286, 35683-35688.]; Taylor et al., 2011[Taylor, J. D., Zhou, Y., Salgado, P. S., Patwardhan, A., McGuffie, M., Pape, T., Grabe, G., Ashman, E., Constable, S. C., Simpson, P. J., Lee, W. C., Cota, E., Chapman, M. R. & Matthews, S. J. (2011). Structure, 19, 1307-1316.]; Lyu et al., 2014[Lyu, K., Ding, J., Han, J.-F., Zhang, Y., Wu, X.-Y., He, Y.-L., Qin, C.-F. & Chen, R. (2014). J. Virol. 88, 3114-3126.]; Miwa et al., 2016[Miwa, K., Kojima, R., Obita, T., Ohkuma, Y., Tamura, Y. & Mizuguchi, M. (2016). J. Mol. Biol. 428, 4258-4266.]; Hong et al., 2016[Hong, L., Jain, N., Cheng, X., Bernal, A., Tyagi, M. & Smith, J. C. (2016). Sci. Adv. 2, e1600886.]). 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[Wälti, M. A., Ravotti, F., Arai, H., Glabe, C. G., Wall, J. S., Böckmann, A., Güntert, P., Meier, B. H. & Riek, R. (2016). Proc. Natl Acad. Sci. USA, 113, E4976-E4984.]). 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[Worrall, L. J., Hong, C., Vuckovic, M., Deng, W., Bergeron, J. R. C., Majewski, D. D., Huang, R. K., Spreter, T., Finlay, B. B., Yu, Z. & Strynadka, N. C. J. (2016). Nature (London), 540, 597-601.]; Galkin et al., 2015[Galkin, V. E., Orlova, A., Vos, M. R., Schröder, G. F. & Egelman, E. H. (2015). Structure, 23, 173-182.]; Bartesaghi et al., 2014[Bartesaghi, A., Matthies, D., Banerjee, S., Merk, A. & Subramaniam, S. (2014). Proc. Natl Acad. Sci. USA, 111, 11709-11714.]; Chua et al., 2016[Chua, E. Y. D., Vogirala, V. K., Inian, O., Wong, A. S. W., Nordenskiöld, L., Plitzko, J. M., Danev, R. & Sandin, S. (2016). Nucleic Acids Res. 44, 8013-8019.]; von der Ecken et al., 2016[Ecken, J. von der, Heissler, S. M., Pathan-Chhatbar, S., Manstein, D. J. & Raunser, S. (2016). Nature (London), 534, 724-728.]) or an XFEL structure at 3.3 Å resolution (Zhou et al., 2016[Zhou, X. E. et al. (2016). Sci Data, 3, 160021.]). 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[Romir, J., Lilie, H., Egerer-Sieber, C., Bauer, F., Sticht, H. & Muller, Y. A. (2007). J. Mol. Biol. 365, 1417-1428.]). 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.

Acknowledgements

This project was supported by the Intramural Research Program of the National Institutes of Health (NIH), National Cancer Institute, Center for Cancer Research.

References

First citationBartesaghi, A., Matthies, D., Banerjee, S., Merk, A. & Subramaniam, S. (2014). Proc. Natl Acad. Sci. USA, 111, 11709–11714.  Web of Science CrossRef CAS PubMed
First citationChua, E. Y. D., Vogirala, V. K., Inian, O., Wong, A. S. W., Nordenskiöld, L., Plitzko, J. M., Danev, R. & Sandin, S. (2016). Nucleic Acids Res. 44, 8013–8019.  Web of Science CrossRef CAS PubMed
First citationEcken, J. von der, Heissler, S. M., Pathan-Chhatbar, S., Manstein, D. J. & Raunser, S. (2016). Nature (London), 534, 724–728.  CrossRef CAS PubMed
First citationGalkin, V. E., Orlova, A., Vos, M. R., Schröder, G. F. & Egelman, E. H. (2015). Structure, 23, 173–182.  CrossRef CAS PubMed
First citationHenderson, J. N., Kuriata, A. M., Fromme, R., Salvucci, M. E. & Wachter, R. M. (2011). J. Biol. Chem. 286, 35683–35688.  Web of Science CrossRef CAS PubMed
First citationHong, L., Jain, N., Cheng, X., Bernal, A., Tyagi, M. & Smith, J. C. (2016). Sci. Adv. 2, e1600886.  CrossRef PubMed
First citationLyu, K., Ding, J., Han, J.-F., Zhang, Y., Wu, X.-Y., He, Y.-L., Qin, C.-F. & Chen, R. (2014). J. Virol. 88, 3114–3126.  CrossRef PubMed
First citationMiwa, K., Kojima, R., Obita, T., Ohkuma, Y., Tamura, Y. & Mizuguchi, M. (2016). J. Mol. Biol. 428, 4258–4266.  CrossRef CAS PubMed
First citationMorris, R. J. & Bricogne, G. (2003). Acta Cryst. D59, 615–617.  Web of Science CrossRef CAS IUCr Journals
First citationRomir, J., Lilie, H., Egerer-Sieber, C., Bauer, F., Sticht, H. & Muller, Y. A. (2007). J. Mol. Biol. 365, 1417–1428.  Web of Science CrossRef PubMed CAS
First citationSheldrick, G. M. (1990). Acta Cryst. A46, 467–473.  CrossRef CAS Web of Science IUCr Journals
First citationTaylor, J. D., Zhou, Y., Salgado, P. S., Patwardhan, A., McGuffie, M., Pape, T., Grabe, G., Ashman, E., Constable, S. C., Simpson, P. J., Lee, W. C., Cota, E., Chapman, M. R. & Matthews, S. J. (2011). Structure, 19, 1307–1316.  Web of Science CrossRef CAS PubMed
First citationWälti, M. A., Ravotti, F., Arai, H., Glabe, C. G., Wall, J. S., Böckmann, A., Güntert, P., Meier, B. H. & Riek, R. (2016). Proc. Natl Acad. Sci. USA, 113, E4976–E4984.  PubMed
First citationWorrall, L. J., Hong, C., Vuckovic, M., Deng, W., Bergeron, J. R. C., Majewski, D. D., Huang, R. K., Spreter, T., Finlay, B. B., Yu, Z. & Strynadka, N. C. J. (2016). Nature (London), 540, 597–601.  CrossRef CAS
First citationZhou, X. E. et al. (2016). Sci Data, 3, 160021.  CrossRef PubMed

© International Union of Crystallography. Prior permission is not required to reproduce short quotations, tables and figures from this article, provided the original authors and source are cited. For more information, click here.

Journal logoSTRUCTURAL
BIOLOGY
ISSN: 2059-7983
Follow Acta Cryst. D
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds