[3dem] published B factors

Sun Aug 30 06:59:46 PDT 2020

Hi Alexis,

Just a small clarification: for the urease and apoferritin data collected
in Basel, the B-factors estimated from the amplitude spectrum (i.e.
postprocessing) were from the symmetrized maps, whereas the ResLog
B-factors you reported were from C1 reconstructions. For consistency, I
share below the complete data and plots, with ResLog B-factors for C1 and
symmetrized reconstructions. I am intrigued by their difference.

Urease
Resolution (FSC 0.143): 1.98 Å
Sharpening B-factor: -38 Å^2
Reconstruction ("ResLog") B-factor: 64.1 Å^2 (C1) and 71.5 Å^2 (T)

Apoferritin
Resolution (FSC 0.143): 1.96 Å
Sharpening B-factor: -50 Å^2
Reconstruction ("ResLog") B-factor: 74.0 Å^2 (C1) and 114.3 Å^2 (O)

Best wishes,

--
Ricardo Diogo Righetto

Em dom., 30 de ago. de 2020 às 08:05, Takanori Nakane <
tnakane at mrc-lmb.cam.ac.uk> escreveu:

> Hi Alexis,
>
> The B factor of 2.3 is not the value that made the spectrum flat.
> The value estimated by PostProcess was 22.3. However, this was blurred by
> 20
> before input into REFMAC. Thus, 2.3 in the "Refinement" table.
>
> The reason we need some blurring before model refinement is as follows.
>
> Wilson plot for crystallography is calculated after taking the resolution
> dependency of atomic scattering factors into account
> (see capital sigma in
> https://urldefense.com/v3/__https://smb.slac.stanford.edu/facilities/software/ccp4/html/pxmaths/bmg10.html__;!!Mih3wA!VbzHfREaHa5xs1lUjL_JGaOxMgD9UaTjmdYW60M0pH8wqO08R9mny2J8xHO6I1vSIA$
> ).
> This is not done in RELION's PostProcess. Thus, the value estimated by
> RELION "over-compensates"
> intrinsic resolution fall-off due to electron scattering factors, making
> them like
> normalized structure factors E in crystallography, which are not what
> REFMAC expects.
>
> Also note that some residues have lower flexibility than other residues.
> Sharpening them by a "global" B factor can make their ADPs negative.
>
> Best regards,
>
> Takanori Nakane
>
> On 2020/08/30 0:20, Alexis Rohou wrote:
> > 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 (Å^2 )
> >
> >
> >
> > 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 <mailto:
> 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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> >
>
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