<div dir="ltr">Dear colleagues,<br><div><br></div><div>Thanks to those who replied. Below are a few examples I gathered of structures for which both types of B factors were available.</div><div><br></div><div>Cheers,</div><div>Alexis</div><div><br></div><div><p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif"><br></p><table class="gmail-MsoTableGrid" border="1" cellspacing="0" cellpadding="0" style="border-collapse:collapse;border:none">
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif"> </p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">B factor (Å<sup>2</sup>)</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">Estimation method</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">Reference</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">In situ bacterial 70S ribosomal subunit at 3.7 Å</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">5</p>
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif"> </p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">Amplitude spectrum<span style="background:yellow"></span></p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">(Tegunov <i>et
al.</i>, 2020)
and pers. comm. from D. Tegunov</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">86</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">ResLog</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">Mouse apoferritin at 1.22 Å</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">2.3</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">Amplitude spectrum</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">(Nakane <i>et al.</i>,
2020)</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">32.5</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">ResLog</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">Urease at 1.98 Å</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">38</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">Amplitude spectrum</p>
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<td width="216" rowspan="2" valign="top" style="width:2.25in;border-top:none;border-left:none;border-bottom:1pt solid windowtext;border-right:1pt solid windowtext;padding:0in 5.4pt">
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">(Righetto <i>et
al.</i>, 2020)
and pers. comm. from R. Righetto </p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">64.1</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">ResLog</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">Apoferritin at 1.96 Å</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">50</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">Amplitude spectrum</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">Pers. comm. from R. Righetto</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">74</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">ResLog</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">Mycobacterial secretion system ESX-3 dimer at 3.8 Å</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">101</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">Amplitude spectrum</p>
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<td width="216" rowspan="2" valign="top" style="width:2.25in;border-top:none;border-left:none;border-bottom:1pt solid windowtext;border-right:1pt solid windowtext;padding:0in 5.4pt">
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">(Famelis <i>et
al.</i>, 2019)
and pers. comm. from A. Rivera Calzada</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">144</p>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">ResLog</p>
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</tbody></table><p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif"><br></p>
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">Famelis, N. <i>et al.</i> (2019) ‘Architecture of the mycobacterial type
VII secretion system.’, <i>Nature</i>, 576(7786), pp. 321–325. doi:
10.1038/s41586-019-1633-1.</p>
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">Merk, A. <i>et al.</i>
(2020) ‘1.8 Å resolution structure of β-galactosidase with a 200 kV CRYO ARM
electron microscope’, <i>IUCrJ</i>. International Union of Crystallography,
7(4), pp. 1–5. doi: 10.1107/s2052252520006855.</p>
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">Nakane, T. <i>et al.</i>
(2020) ‘Single-particle cryo-EM at atomic resolution’.</p>
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">Righetto, R. D. <i>et al.</i>
(2020) ‘High-resolution cryo-EM structure of urease from the pathogen Yersinia
enterocolitica’, <i>bioRxiv</i>, p. 2020.04.28.065599. doi:
10.1101/2020.04.28.065599.</p>
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:Calibri,sans-serif">Tegunov, D. <i>et al.</i>
(2020) ‘Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic
complex at 3 . 7 Å inside cells’.</p>
<p class="MsoNormal" style="margin:0in 0in 0.0001pt 32pt;font-size:12pt;font-family:Calibri,sans-serif"> </p></div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Jul 5, 2020 at 11:49 AM Alexis Rohou <<a href="mailto:a.rohou@gmail.com">a.rohou@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Dear colleagues,<div><br></div><div>If you know of a publication that includes, for the same dataset, both: </div><div><br></div><div>(1) an estimate of the "sharpening" B factor (i.e. based on the radial amplitude spectrum of a 3D reconstruction) as well as </div><div>(2) the B factor estimated from a plot of resolution as a function of number of particles (also known as ResLog plot), </div><div><br></div><div>... would you please point me to relevant citation(s)?</div><div><br></div><div>Thanks!</div><div>Alexis</div><div><br></div><div>PS. Feel free to reply to me directly if you prefer - I can summarize findings to the list in a few days</div></div>
</blockquote></div>