By the way. Does anyone out there have a unit cell search engine still
running? The two mentioned on this thread so far:
ContaMiner: https://strube.cbrc.kaust.edu.sa/contaminer/
and SIMBAD: http://ccp4serv7.rc-harwell.ac.uk:8080/testserv/
seem to both be down. And the other one I know about
nearest-cell: https://app.strubi.ox.ac.uk/nearest-cell/nearest-cell.cgi
is up, but doesn't seem to be working. Can't find 4y42 using Dong
Xiao's cell below.
Perhaps the maintainers of these pages could chime in?
-James Holton
MAD Scientist
On 6/17/2017 10:43 AM, James Holton wrote:
The reduced (aka "Niggli") cell for your case is 82.8246 88.2997
82.8246 98.8892 110.5181 117.0456
You can get this using "tracer" or "othercell" in the CCP4 suite.
I keep a local table of reduced cells from the PDB that I update
periodically, and the closest one to yours in that list is:
4y42 82.5 88.0 82.5 99 110 117 cyanate hydratase
This was deposited in P1, but if you download the data and feed it to
Pointless, it is quite confident that the true space group is actually
C2. There are 10 chains in the ASU so there may be some pseudo
symmetry going on. The paper reporting 4y42 describes it as a "
serendipitous crystallization".
What happens if you try to refine your data against the model
deposited as 4y42?
Hope that helps,
-James Holton
MAD Scientist
On 6/17/2017 12:07 AM, dongxiaofei wrote:
Dear ALL,
I got two kinds of crystals of different proteins ,but there are many
similarities.
The shape of the crystals are similar, the cell parameters are also
similar :
protein A , 136.12 94.398 89.476 90 125.479 90 , Space
group C 1 2 1 and
protein B , 136.14 94.369 89.115 90 125.495 90 , Space
group C 1 2 1.
protein A has a NMR structure ,but Rfree always high above 50% after
molecular replacement , protein B’s Rfree is also above 50% .
So I am wonder if these crystals are the result of debris of proteins
, because the growth of the crystals needs more than half a year . I
am sure the two proteins are different and crystals respectively
come from different proteins
Any insights will be really appreciated.
Thanks
Dong Xiao
