On 03/13/2014 10:55 AM, Keller, Jacob wrote:
Unless you are interested in finding curious objects, what would you do with
protein quasicrystal? The practices of macromolecular crystallography is about
determining 3-dimensional structure of objects being crystallized. Protein
quasicrystal are really unlikely to diffract to high enough resolution, and
even ignoring all other practical aspects, like writing programs to solve such
a structure, chances of building an atomic model are really slim.
Right, if crystallography is seen as purely a tool for biology I agree. As for
curious objects, I think almost all profound breakthroughs come from
unadulterated curiosity and not desire for some practical end. Not sure why a
priori this should be so, but just consider your favorite scientific
breakthrough and whether the scientist set out to make the discovery or not.
Some are, but most are not, I think. Maybe aperiodic protein crystals have some
important function in biology somewhere, or have unforeseen materials science
properties, analogous to silk or something.
This is easy to test by analyzing diffraction patterns of individual crystals.
In practice, the dominant contribution to angular broadening of
diffraction peaks is angular disorder of microdomains, particularly in
cryo-cooled crystals.
However, exceptions do happen, but these rare situations need to be
handled on case by case basis.
The interpretation of the data presented in this article is that variation in
unit cell between microcrystals induce their spatial misalignment. The data do
not show variation of unit cell within individual microscrystalline domains.
Tetragonal lysozyme can adopt quite a few variations of the crystal lattice
during cryocooling. Depending on the conditions used, resulting mosaicity can
vary from 0.1 degree (even for 1mm size crystal) to over 1. degree.
Consequently, measured structure factors from a group of tetragonal lysozyme
crystal can be quite reproducible, or not. As a test crystal, it should be
handled with care.
1 degree mosaicity is not an impediment to high quality measurements. However,
high mosaicity tends to correlate with presence of phase transitions during
cryo-cooling. If such transition happen during cryo-cooling, crystals of the
same protein, even from the same drop, may vary quite a lot in terms of
structure factors. Additionally, even similar values of unit cell parameters
are not guarantee of isomorphism between crystals.
So I think you are saying that tetragonal lysozyme is an atypical case, and that normally
the main contributor to the fitted parameter "mosaicity" is the phenomenon of
microdomains shifted slightly in orientation. Maybe we can get the author to repeat the
study for the other usual-suspect protein crystals to find out the truth, but the score
currently seems to be 1-0 in favor of cell parameter shifts versus microcrystal
orientation...
No, I claim that the particular crystal studied by Colin Nave (Acta Cryst. 1998,
D54: 848) is atypical case. I processed myself hundreds of tetragonal lysozyme
data sets acquired on crystals grown and mounted by various people, so I believe
that my experience defines better a typical case.
The second reference, nicely provided by Colin, does not make the conclusion
that "dominant imperfection appeared to be a variation in unit-cell dimensions
in the crystal", but rather states that "The analysis further suggests that LT
disorder is governed by variability inherent in the cooling process combined
with the overall history of the crystal."
As you can see on the figure 5A in Juers at al, 2007, the mosaicity is a
dominant component of the reflection width for resolution higher than 8A.
Only for very low resolutions one can see the effect of unit cell changes.
What is important is that the crystal analyzed had a very low mosaicity: less
than 0.02 degree before cryo-cooling and less than 0.1 degree after
cryo-cooling. The mosacity after cryo-cooling is definitely below typical values.
One has to remember that not only unit cell parameters are different for
different microdomains, but also their structure factors will vary and can
change quite a lot. Cryo-cooled crystals definitely can have high degree of
internal non-isomorphism resulting from this effect.
Zbyszek
--
Zbyszek Otwinowski
UT Southwestern Medical Center
5323 Harry Hines Blvd., Dallas, TX 75390-8816
(214) 645 6385 (phone) (214) 645 6353 (fax)
zbys...@work.swmed.edu
