Dear all, just a super dummy question: I treated a protein with
trypsin, found the protein being degraded into two well-define
fragments, ran a sizing column to find them co-elute, sent the peak
fraction for mass-spec, got the two masses. Now here is the question -
is there any program readily ava
Hi,
If you have density for the protein and the DNA and the density for
the protein is correct and you see left-handed DNA density, then I
suppose you are seeing Z-DNA?
Doesn't seem like a problem of incorrect enantiomorph if your protein
density is fine. You can pull out a Z-DNA structure
Hello Ruchi,
I know that when you use non-crystallographic averaging there is a possibility
of the starting with positive density and ending up with negative, the
enantiomorph, or the negative enantiomorph density. In order to shift back to
the correct phases you can apply a simple formula. Th
Dear All,
We are working with a DNA binding protein with 4 Zn sites in in ASU. Using SnB
and then CNS we were able to get a map using MAD phasing and could visualize
the density for the double helix of the DNA but it was a left handed spiral
instead of the usual right handed one. The space group
hi,
I have installed ccp4mg as part of the ccp4 distribution on FC6 x86_64 linux.
when I try to use ccp4mg I get (no errors during installation):
--
Traceback (most recent call last):
File "", line 2, in ?
File "/usr/local/src/CCP4/ccp4mg-1.0/python/ui/history.py", line 16, in ?
I've found that crystallization in sitting drops under oil dramatically reduces
the no. of nucleation events and increases the overall crystal size. Now, if
the increased crystal size helps improve diffraction is something to be tested.
Among the many other suggestions...
Raji
-Includ
MRC Laboratory of Molecular Biology - Cambridge
Scientific programmer
A position is available for a programmer to continue the development
of a new Graphical User Interface for a widely used program to process
X-ray diffraction data from crystals of biological macromolecules
(MOSFLM). The interfa
Not a contradiction at all :) If the protein supply is adequate - this is
a perfectly good approach to explore. I simply forgot to mention it.
I've also not mentioned engineering the protein's surface (works really
well for us because we have secret ways to do this, learned from ancient
and myster
In addition to trying lower concentrations of PEG and protein, you might
consider whether aggregation in your protein stock or vibration in your
crystallization environment are contributing to the problem, and how
they might be minimized. It might be obvious, but we have found that it
is important
You said you tried macroseeding, but what about microseeding? It works
quite well in many cases. Just don't forget that you should find a zone
were nucleation does not happen before you seed. Take a look at this paper:
Bergfors, T. (2003) Seeds to Crystals, J. Struct. Biol., 142, 66-76.
There
Hi Jobi
Sounds like you need to explore your protein vs PEG concentration, and my
guess (directly contradicting Artem's) is that chances are you need to pump
[protein] way up and drop [PEG] way down.
Like in [protein]=>30-40mg/ml, [PEG]<=2-4%. Often people don't go into that
range when setti
1) Why do you think there is twinning? If you label a structure whose
true spacegroup is H32 as having SG H3, then some of the twinning
analyses report that this is consistent with perfect twinning..
I believe the graphs of the moments from TRUNCATE give a true indicator.
Ditto the latest SFCH
Post-doctoral positions are available in the Protein Design group
at Yokohama City University. Projects include beta helical bacterial
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