[3dem] B-factors

[Henning Stahlberg]

Dear Colleagues,

There are two B-factors used in cryo-EM:

Rosenthal and Henderson, JMB (2003) discuss the Guinier plot, where the amplitude falloff beyond 10A resolution can be fitted with a B-factor that has the unit "Angstromˆ2".
They also discuss the dependency of the resolution d (in Angstroem) on the number # of particles, and provide the basis for a ResLog B-factor, which is obtained from the slope of 1/dˆ2 as a function of ln(#).  The numbers of particles needed to reach a resolution "d" is then obtained with:
# = (1/Nasym) * (<S>/<N>)ˆ2 * (30 pi) / (N_e * sigma_e * d) * exp(B / (2 * dˆ2))
The B-factor also in this case is defined as in Angstromˆ2.

Stagg et al., JSB (2014) define a dependency of the resolution d from ln(#), with
d = constant * ln(#) + constant.
So, here, “d” is linear, not to the square. Their ResLog B-factor is then presumably obtained from the first "constant" in that equation, therefore in Angstrom,  not Angstromˆ2.  
This is also implemented in CryoSPARC, which also plots 1/d as a function of ln(#).
But other papers, such as Yip et al. and Holger Stark, Nature (2020) discuss the ResLog B-factor in Aˆ2 again.

It is interesting for a map to provide all three, the FSC 0.143, the Sharpening B-factor in Aˆ2, and the Reconstruction ("ResLog") B-factor in Aˆ2.

But, what is the most commonly used definition of the ResLog B-factor, A or Aˆ2 ?

Best wishes,

Henning.

Henning Stahlberg
Laboratory of Biological Electron Microscopy
Institute of Physics, School of Basic Sciences, EPFL, and
Dep. of Fund. Microbiology, Faculty of Biology and Medicine, UNIL,
Cubotron, BSP421, 1015 Lausanne, Switzerland
https://urldefense.com/v3/__https://lbem.ch__;!!Mih3wA!He8RNad9-usi4V76A6bilma8i0ypnwt1U80fxDsSqpHDIfUZKGI_ft-uqv-vt7uS2afD77_BWpZnsmapEJYkinMjcYW-0HQ$ , +41 21 693 45 07