[3dem] Which resolution?

[Egelman, Edward H (ehe2n)]

I had studiously avoided getting involved in this thread which might lead to a long exchange with Marin about the history, significance and ontological status of the FSC, but I will suggest a paper that while dated addresses some of these isssues:

Subramaniam, S., Earl, L.A., Falconieri, V., Milne, J.L., and Egelman, E.H. (2016). Resolution advances in cryo-EM enable application to drug discovery. Curr Opin Struct Biol 41, 194-202.
Abstract

The prospect that the structures of protein assemblies, small and large, can be determined using cryo-electron microscopy (cryo-EM) is beginning to transform the landscape of structural biology and cell biology. Great progress is being made in determining 3D structures of biological assemblies ranging from icosahedral viruses and helical arrays to small membrane proteins and protein complexes. Here, we review recent advances in this field, focusing especially on the emerging use of cryo-EM in mapping the binding of drugs and inhibitors to protein targets, an application that requires structure determination at the highest possible resolutions. We discuss methods used to evaluate the information contained in cryo-EM density maps and consider strengths and weaknesses of approaches currently used to measure map resolution.

We discuss that FSC is NOT a measure of resolution, it is a measure of reproducibility. We give examples for structures with symmetry where one can impose the wrong symmetry and get a better FSC than with the correct symmetry (this is also discussed in Egelman, E.H. 2014. Ambiguities in helical reconstruction. Elife 3.). While the map looks like garbage, the FSC does not care as the garbage is highly reproducible. As to actually looking at the map, I would agree with previous people who have commented or implied that the gold standard in x-ray crystallography has always been the visual appearance and interpretability of the map, and not some single metric.
Regards,
Ed


Edward Egelman
Harrison Distinguished Professor
Department of Biochemistry and Molecular Genetics
University of Virginia
phone: 434-924-8210
fax: 434-924-5069
egelman at virginia.edu
www.people.virginia.edu/~ehe2n<http://www.people.virginia.edu/~ehe2n>

From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Pawel Penczek <Pawel.A.Penczek at uth.tmc.edu>
Date: Thursday, February 13, 2020 at 8:42 AM
To: 3dem <3dem at ncmir.ucsd.edu>
Subject: [3dem] Which resolution?

Dear Teige,

I am wondering whether you are familiar with

Resolution measures in molecular electron microscopy.
Penczek PA. Methods Enzymol. 2010.
Citation

Methods Enzymol. 2010;482:73-100. doi: 10.1016/S0076-6879(10)82003-8.

You will find there answers to all questions you asked and much more.

Regards,
Pawel Penczek

Regards,
Pawel
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