Latest Trends Q's

Raman barani at
Wed Oct 30 11:36:45 EST 1996

>From: junko at (AutorCasi)
>Newsgroups: bionet.xtallography,sci.techniques.xtallography
>Subject: Latest Trends Q's
>Date: Wed, 30 Oct 1996 14:25:49 GMT
>I would appreciate some help with a few questions I have about xtallography.
>Any references or hints to ref'd journals would especially be nice.  Please
>excuse the naivete of my word-usage and questions.

Welcome to the society of x-ray crystallographers!

>1) What is the most recent problem/dilemma in phase retrieval wrt

The most recent as well as the oldest problem remain the same.
How do you get the phases from a macromolecular diffraction?
You should write to the best person working on this problem - 
Jerome Karle at NIH.

>2) When collecting a diffraction/scattering pattern, how much
>molecular/protein hinge motion is averaged out (-+10Ang?)?  And how much
>degradation or "blurring" does this motion cause in the pattern-image?

If you are referring to 'correlated motion', I guess it affects only high
resolution reflections which fall off in intensity.

>3) Is Isomorphic Replacement still the most widely used technique for
>acquiring phase information? If not, what is the lastest technique?  If so,
>how much distortion/blurring/degradation does the diffused metal ion cause in
>the pattern?

Multiple isomorphism, by theory, provides phases with only a sign error.
Therefore it is a powerful alternative to x-ray lasers. 
Molecular replacement has been used, in recent times, for many
structures; but the method lacks a rigour owing to a theoretical
possibility of model-bias. Anamolous scattering has occasionally been
used, successfully, to solve structures. 

No distortion or degradation or blurring expected due to different metal 
ion binding.  Often the quality of the crystal decreases during substitution 
of the metal ion, either due to a harsh treatment or due to the protein's
inherent dislike for that metal ion which may alter the coordination
sphere geometry.

>4) What species of protein or virii have been crystallized, yet whose
>structure has not been solved because of motion? 

As far as I know, bulk motions within a crystal do not alter the
diffraction quality, for the purposes of structure solution.
Problems in solving a structure have not depended on any 'motion'
in a crystal.

>5) In enzyme catalysis, how does one acquire a good "frozen" diffraction
>pattern of an intermediate or other step during the process/motion of
>catalysis?  Is there blurring?

It is called 'transition state'.  During a catalysis, atleast
three competing species are involved:

 Let E = Enzyme;  S1 = starting substrate;  S2= Catalysed substrate.

 E + S1  <--->   E.S1   <--->  E + S2

 Biochemists try to saturate/populate species E.S1  by oversaturating
 S1 and S2, so that E.S1 cannot proceed in either direction.
 Removing the crystal from the solution, (and often freezing it)
 prevents further reaction. 

>6) Any other thoughts about diffraction pattern degradation/blurring?

Quality of the diffraction pattern degrades when exposed to x-rays.
This is due to release of free-radicals. Even exposing a crystal into
x-ray for a few seconds is sufficient to start the decay process that
will continuously degrade the crystalline order, without further exposure.
This is why the diffraction patterns are recorded within the shortest
possible duration, like in a synchrotron. 

Quality of crystals often degrade during substrate binding too. Subjecting
a grown crystal to any further treatment is likely to only reduce its
ability to diffract. Freezing has been shown to retain the ability
to diffract but not shown to improve its quality.

>Thanks much.

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