[3dem] published B factors

Sun Aug 30 15:10:53 PDT 2020

Thanks Ricardo!

I have amended my table to use the B factors estimated from the
symmetry-imposed experiments in both cases.

I agree that the differences in ResLog B factors between the C1 and
symmetry-imposed experiments are interesting.

Cheers,
Alexis

On Sun, Aug 30, 2020 at 6:59 AM Ricardo Righetto <ricardorighetto at gmail.com>
wrote:

> 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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