[3dem] published B factors

[Alexis Rohou]

Dear colleagues,

Thanks to those who replied. Below are a few examples I gathered of
structures for which both types of B factors were available.

Cheers,
Alexis




B factor (Å2)

Estimation method

Reference

In situ bacterial 70S ribosomal subunit at 3.7 Å

5



Amplitude spectrum

(Tegunov *et al.*, 2020) and pers. comm. from D. Tegunov

86

ResLog

Mouse apoferritin at 1.22 Å

2.3

Amplitude spectrum

(Nakane *et al.*, 2020)

32.5

ResLog

Urease at 1.98 Å

38

Amplitude spectrum

(Righetto *et al.*, 2020) and pers. comm. from R. Righetto

64.1

ResLog

Apoferritin at 1.96 Å

50

Amplitude spectrum

Pers. comm. from R. Righetto

74

ResLog

Mycobacterial secretion system ESX-3 dimer at 3.8 Å

101

Amplitude spectrum

(Famelis *et al.*, 2019) and pers. comm. from A. Rivera Calzada

144

ResLog


Famelis, N. *et al.* (2019) ‘Architecture of the mycobacterial type VII
secretion system.’, *Nature*, 576(7786), pp. 321–325. doi:
10.1038/s41586-019-1633-1.

Merk, A. *et al.* (2020) ‘1.8 Å resolution structure of β-galactosidase
with a 200 kV CRYO ARM electron microscope’, *IUCrJ*. International Union
of Crystallography, 7(4), pp. 1–5. doi: 10.1107/s2052252520006855.

Nakane, T. *et al.* (2020) ‘Single-particle cryo-EM at atomic resolution’.

Righetto, R. D. *et al.* (2020) ‘High-resolution cryo-EM structure of
urease from the pathogen Yersinia enterocolitica’, *bioRxiv*, p.
2020.04.28.065599. doi: 10.1101/2020.04.28.065599.

Tegunov, D. *et al.* (2020) ‘Multi-particle cryo-EM refinement with M
visualizes ribosome-antibiotic complex at 3 . 7 Å inside cells’.





On Sun, Jul 5, 2020 at 11:49 AM Alexis Rohou <a.rohou at gmail.com> wrote:

> Dear colleagues,
>
> If you know of a publication that includes, for the same dataset, both:
>
> (1) an estimate of the "sharpening" B factor (i.e. based on the radial
> amplitude spectrum of a 3D reconstruction) as well as
> (2) the B factor estimated from a plot of resolution as a function of
> number of particles (also known as ResLog plot),
>
> ... would you please point me to relevant citation(s)?
>
> Thanks!
> Alexis
>
> PS. Feel free to reply to me directly if you prefer - I can summarize
> findings to the list in a few days
>
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