On Thu, Mar 07, 2019 at 02:32:53PM -0600, Murpholino Peligro wrote:
> Let's say I have a protein crystal from which I collected 30 datasets. If I
> plot the unit cell volume per dataset the volume rises.
You also have to be sure that
(1) there is no significant energy drift during those experiments
(which if not modelled could be compensated by a change in
refined cell dimensions)
(2) each dataset has been collected identically (over the same part
of the crystal) and contains enough observations to give a stable
refinement of your cell parameters
I would also check the values of crystal-detector distance as a
function of dose - since these should stay stable and not drift as
well. Sometimes instrumentation changes/drifts can be compensated by a
change in refined cell dimensions while the physical cell within the
crystal actually stays static.
Assuming you have high quality data for each of those datasets, a good
test is to refine your model to convergence against each of those and
see if the final (standard) bonds are systematically shorter or longer
than the expected values (e.g. Engh&Huber for protein). WhatCheck does
a check for that and correlates it with a nice suggestion about wrong
cell parameters ... which can highlight e.g. errors in energy or
wavelength values as written by beamlines into image headers ;-)
Cheers
Clemens
> My question is: Is there a rule of thumb of some sort* to consider the
> initial/final datasets isomorphous still?
>
> * Something like if the unit cell volume changes more than 1% then the
> crystal is not isomorphous.
>
> My second question is: Meents already said that the unit cell volume
> expansion is a consequence of hydrogen gas building up inside the crystal.
> But...what if the unit cell volume decreases? Is there an explanation for
> that?
>
>
> Thank you very much.
>
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* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
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* Cambridge CB3 0AX, UK www.globalphasing.com
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