Woops!, yes Randy, I should have written B = 8*pi^2*<u>^2, not
8*pi*<u>^2 in my original response.
Incidentally, the "A factor" of a Lorentzian-distributed atom is 2*pi*w
where "w" is the full-width at half-maximum (FWHM) of the histogram of
displacements.
It is important to remember also that the rms displacement is not the
same as the FWHM of the peak. A Gaussian distribution with rms=1 has a
histogram with FWHM = ~2.35. For example, a carbon atom has a FWHM of
about 0.8 A, which is equivalent to a point atom with a B-factor of ~9
A^2. A carbon atom with a B-factor of 48 A^2 has a FWHM of 2 A.
-James Holton
MAD Scientist
Randy Read wrote:
Just to clarify what Eleanor is saying:
It was pointed out earlier (by James Holton, if I remember correctly?)
that only the vibration in the direction parallel to the diffraction
vector matters. If the mean-squared vibration in that direction is
1A^2, then the B-factor will be about 80A^2 (8*Pi^2 to be precise).
However, people tend to think of mean-square displacements in 3D
space. If the vibration is isotropic, then there is equal vibration
in the two directions perpendicular to the diffraction vector (which
don't affect the falloff of the scattering from that atom), and the
overall mean-square displacement is 3 times the mean-square
displacement in any one direction. So if you're thinking in terms of
3D mean-square displacement, you have to divide by 3 to get the
displacement parallel to the diffraction vector. In that case, an
atom with an overall 3D mean-square displacement of 1A^2 has a
B-factor of about 26A^2 (8*Pi^2/3).
Regards,
Randy Read
On 11 Dec 2008, at 09:39, Eleanor Dodson wrote:
A small molecule crystallography text would give you the formulation
for an ideal case.
A rough guide is that a B factor of 80 is equivalent to a mean
vibration about the coordinate of 1A
But for proteins the B factor becomes the collection bin for all
sorts of other errors - unrecognised multiple conformations, , and
the restraints used make it harder to interpret.
Eleanor
Jacob Keller wrote:
Hello Crystallographers,
does anybody have a good reference dealing with interpretations of
what B-factors (anisotropic or otherwise) really signify? In other
words, a systematic addressing of all of the possible underlying
molecular/crystal/data-collection phenomena which the B-factor
mathematically models?
Thanks in advance,
Jacob
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
*******************************************
------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: + 44 1223 336500
Wellcome Trust/MRC Building Fax: + 44 1223 336827
Hills Road E-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.
www-structmed.cimr.cam.ac.uk
