[ccp4bb] Help in Cell content analysis

[Monica Mittal]

Dear all
i have a small query to ask and seek your suggestions:

I have collected a data for a protein with 324 residues and processed at
its best in P212121. So Matthews suggest 1 mol in ASU with expected Mol.
weight of 43 kDa with sovent content of 58% and 2 mol./ASU with 18% solvent
content. However the data suggest possibility of translational NCS so i
think i should ask for two molecules so that both get corrected for NCS.
However for 2 mol./ASU, Matthewssuggests a total mol. weight of 52 kDa. So
how to decide which way to proceed for MR?

Thanks
Monica

Re: [ccp4bb] Help in Cell content analysis

[Eleanor Dodson]

That is puzzling.

18% solvent is not common and you would expect very strong diffraction with
such a low solvent content.

one possibility is that the NC symmetry is parallel to a crystal axis and
is making monoclinic data appear to have an extra 2-fold axis. (There is a
case I have heard of wherethe SG turned out to be P21 and not P2i2i2i -
done by Michael Isupov.  You could probably find a reference to it)

I would look carefully at the pointless summary of the quality of the
symmetry operators. If one 2-fold is better than the other two maybe
process the data with that 2 fold only..

Of course another possibility is that the protein has been chewed up in
crystallisation!
Do you have an MR model?
Eleanor

Re: [ccp4bb] Help in Cell content analysis

[Zbyszek Otwinowski]

If your translational NCS is defined by a vector that does not correspond
to lattice centering, i.e. has numbers different from 0 or 0.5, this is
likely a case of order-disorder. Most such cases can be easily diagnosed
by abnormal patterns in spot shape, e.g. every second reflection has a
non-Bragg streak associated with it.
Apparent dense packing, 18% of the solvent, is likely to arise from random
packing of molecules in alternative positions within the unit cell, where
every second position is occupied. This randomness can be cross-correlated
between cells, and this will produce a diffuse scattering.
An alternative explanation is that you crystallised a proteolitic fragment
of your protein.

Zbyszek Otwinowski

> Dear all
> i have a small query to ask and seek your suggestions:
>
> I have collected a data for a protein with 324 residues and processed at
> its best in P212121. So Matthews suggest 1 mol in ASU with expected Mol.
> weight of 43 kDa with sovent content of 58% and 2 mol./ASU with 18%
> solvent
> content. However the data suggest possibility of translational NCS so i
> think i should ask for two molecules so that both get corrected for NCS.
> However for 2 mol./ASU, Matthewssuggests a total mol. weight of 52 kDa. So
> how to decide which way to proceed for MR?
>
> Thanks
> Monica
>


Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel. 214-645-6385
Fax. 214-645-6353