[phenixbb] Asymmetric unit content
Roger Rowlett
rrowlett at colgate.edu
Mon Dec 12 07:28:13 PST 2016
The Matthews coefficient is relatively efficient at distinguishing
likely ASU content for N<=4. However, the probability distribution of
the solvent content of protein crystals is broad enough that it is
difficult to distinguish from the Matthews coefficient alone if an ASU
has say, 4 or 6 (or 6 or 8) molecules in the ASU. Realistically, the
Matthews coefficient is going to give you a range of likely
possibilities. 1 vs. 2 is easy to distinguish. Not so 4 vs. 5 vs. 6.
Ultimately, you have to look at your MR solution and the molecule
packing in the unit cell. Said packing should make chemical sense, and
reveal highly symmetric solvent channels. A periodic "gap" in your
crystal packing, supported by un-filled electron density, is a clue that
something might be missing. At 7A resolution, I would suspect that the
electron density clarity would not be terrific.
5 molecules in the ASU seems a bit odd to me. (4 or 6 seems more
probable.) If it is 5 molecules, one of the molecules would have to be
on a symmetry axis, completing a "symmetry" dimer, with two other dimers
in the ASU? I've seen 6 molecules in the ASU in C2, with one tetramer
and one half-tetramer on the symmetry axis. When solving that one, the
Matthews Probability calculator insisted that there were 4 molecules in
the ASU. Turned out to be 6. I initially placed 4 molecules in the ASU,
and saw a clear crystal-packing gap for another dimer that would fit
neatly next to the symmetry axis.
_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowlett at colgate.edu
On 12/12/2016 9:52 AM, oleg at quantumbioinc.com wrote:
> Compute Matthews coefficient.
> e.g. using
> http://www.ruppweb.org/mattprob/default.html
>
> Oleg
>
>
>
> -----Original Message-----
> From: "Sharan Karade" <sharankarade at gmail.com>
> Sent: Sunday, December 11, 2016 6:05am
> To: phenixbb at phenix-online.org
> Subject: [phenixbb] Asymmetric unit content
>
> _______________________________________________
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> phenixbb at phenix-online.org
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> Unsubscribe: phenixbb-leave at phenix-online.orgDear all,
>
> I have solved the structure in C121 space group, having five
> molecules in asymmetric unit, my supervisor have doubt about the fifth
> molecule becoz of poor density fit, if i delete the fifth molecule, there
> is a space for the molecule and crystal is not continuous, i calculated
> difference map from Phenix by deleting fifth molecule and got the Map
> showing presence of molecule. My supervisor want me to get SetMet data, but
> crystals are diffracting poor (7A). Is there any way to convince my guide.
>
>
> advance thanks for valuable suggestions.
>
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