Hi Teresa,
As Eleanor has mentioned, you should probably check out other space
groups. Xtriage gives a lot of great information and many plots to
inspect. But, if you do not know what the plots mean and just look at
the results that say the twin fraction is 0.48 you can get into some
Is this a joke or are you serious??? Hopefully you haven't actually
started shooting people with highly focused X-rays...
Jon
On 07/12/2013 10:14 AM, diptimayee mishra wrote:
Dear All,
Can anyone please tell me regarding the harmful effects of X-ray , we
are using for protein
Niu,
Could you give me some information about when you came to NE-CAT and
I will tell you the beam center. We can do this off the CCP4BB. My email
is schue...@anl.gov
Thanks,
Jon
On 01/17/2013 03:19 PM, Niu Tou wrote:
Hi colleagues,
We have collected several datasets at APS with
Phenix does this
(http://www.phenix-online.org/documentation/autosol.htm#anch125)
Phaser-EP
(http://www.phaser.cimr.cam.ac.uk/index.php/Experimental_Phasing#Combined_MR_and_SAD_Phasing)
and SHELX using an experimental version you have to get from George
Sheldrick.
Jon
--
Jonathan P.
I forgot to mention... there are two ways of calculating the phases in
Phenix, try both ways because the maps can look very different.
Jon
--
Jonathan P. Schuermann, Ph. D.
Beamline Scientist
NE-CAT, Building 436E
Advanced Photon Source (APS)
Argonne National Laboratory
9700 South Cass Avenue
I have used and worked on both the Bio-Rad and Akta systems. It is
really a matter of opinion, but they both get the job done.
Exterior:
The Akta systems look nice with metal exteriors while the Bio-Rads look
a little cheap being plastic. Both are really heavy, though.
Interior:
Once you
I am sure this has happened many many times before but I cannot find a
reference. I have a protein/DNA complex structure where the protein has
P212121 symmetry, but the DNA only has P21 symmetry. I know its
pseudosymmetry caused by the NCS. Has anyone seen this with protein/DNA
or have a
If I'm not mistaken it is caused by /tmp/'username' not existing or
being writable...
Jon
--
Jonathan P. Schuermann, Ph. D.
Beamline Scientist
NE-CAT, Building 436E
Advanced Photon Source (APS)
Argonne National Laboratory
9700 South Cass Avenue
Argonne, IL 60439
email: schue...@anl.gov
Tel:
Without seeing your NZ or L-test plots, but looking at the logs, your
data does not appear to be twinned. It will not be R32 because the
R-merge is too high. The probable space group is C2. The listed twin
fractions will approach 0.5 if your data has perfect twinning or you
processed in too
Just to add to Phil and Eleanor's response...
I would NOT use Phaser for MR with PTS present. It doesn't handle it
correctly yet, since the likelihood targets don't account for PTS.
Others may be able to explain it better.
Its probably not C-centered (as Eleanor mentions) and you should try
According to the paper, the data was refined in REFMAC in 'twin mode'
which, I believe, calculates the R-factor using a non-conventional
R-factor equation which usually lower than the conventional R-factor. I
believe this is dependent on the twin fraction which wasn't mentioned in
the paper
Fulvio,
We need more info to give advice. First, when you say Rsym is 0.18,
are you talking about in the high res bin or overall? Second, how did
you determine you have twinning? In what space group did you scale your
data? If your data is actually twinned with a high twin fraction, and
cell and try to solve it that way without the pseudo-centering,
especially if the off-origin Patterson peak is large (50% of origin peak).
Jon Schuermann
--
Jonathan P. Schuermann, Ph. D.
Beamline Scientist
NE-CAT, Building 436E
Advanced Photon Source (APS)
Argonne National Laboratory
9700 South
Yang,
There are not any merohedral twin laws, but there are several
pseudomerohedral twinning possibilities. The most common would be a
monoclinic cell with a beta ~90, so it appears orthorhombic. Going the
other way, you could have an orthorhombic cell look tetragonal if A and
B are
Hari,
What twin tests have you run? Results? If your data really is
P43212 and you drop to P212121 you will still have the additional
two-fold operator in your data. An operator is a mathematical operator,
which could be crystallographic or twin.
I never refine a structure with twin
Maybe I am not getting it, but I don't see your problem or question?
What I understand from your message is that you have a protein that
overexpresses, purifies, and crystallizes... where's the problem? We all
wish we had that problem...
Jon
On 02/18/2010 11:49 AM, Armando Albert de la
be although it's supposed to be 29kDa it runs
funny and appears larger in the SDS gel, in that case it would be OK.
If we only had some confirmation that the 43kDa band is the right one
e.g. via Western Blot Anti-His ...
Jürgen
On Feb 18, 2010, at 4:01 PM, Jon Schuermann wrote:
Maybe I am
find the correct SG. Peter or
Andrey will probably chime in here if this is your problem.
HTH,
Jon Schuermann
--
Jonathan P. Schuermann, Ph. D.
Beamline Scientist
NE-CAT, Building 436E
Advanced Photon Source (APS)
Argonne National Laboratory
9700 South Cass Avenue
Argonne, IL 60439
email
Actually, another thing could be going on as well. You show a large
off-origin peak in the Patterson in I422 so you may have
pseudotranslation going on and you processed in the supercell. You could
probably try to reindex choosing fewer spots and get your P422 cell. I
am sure there is some law
Fabien,
The extra density may be from a his-tag or cloning artifacts left over
at the beginning or end of your protein sequence. You may be seeing the
residues coming from a neighboring molecule. I have seen parts of a
C-terminal his-tag ordered in the electron density before.
Jon
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