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[ccp4bb]: spacegroup problem
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I have asked this question once before, but i
think now i have more data and information and
threfore can present my problem in a better way.
I have a set of datasets collected at
synchroton.( native till 1.9 a resolution and four
derivatives till 2.2 A resolution, Hgcl2 HgCN, Pt and
Pb). There is an ambiguity in spacegroup for these
crystals. Denzo gives P tetragonal if allowed to take
the default no. of spots. It gives I tetragonal if the
no. of spots taken for autoindexing are reduced. Same
is the case with automar. Somebody suggested that i
should take two images 90 degrees apart and see. Two
images taken 90 degree apart does reduce the error ,
but the trick remains the same less no. of spots give
I tetragonal and more no. of spots give P tetragonal.
I then tried mosflm. Here i do not know how to change
the no. of spots to be taken and so I treid with
default no. of spots. It gave varying results. It gave
P tetragonal for the native and the Pt. crytal but
gave I tetragonal for the rest of the derivatives.
I have also calculated native patterson till 2.2
a resolution with the P tetragonal mtz file for all
datasets. All the datasets give very large off origin
peak at 1/2, 1/2, 1/2. The origin peak is on an
average ~110 and the one at 1/2, 1/2, 1/2 is about 88.
I looked at h+k+l=2n+1 reflections in the sca
file of P tetragonal. Many reflections are weak but
many are present.
I have an earlier set of datasets( 1 native
till 2.5 and 3 derivatives also till 2.5) collected in
house. These crystals unambiguosly give the spacegroup
as I tetragonal. The cell parameters of both the
datasets (collected in house and those at synchroton)
are the same.
From the data collected in house i could
manage to build a partial model ( a little less than
half of the structure). The heavy atom derivatives
were not very good and that is why i had tried to
collect another datset at the synchroton. My protein
does not have much regular secondary structure and the
phases also not being good i was not sure wether i had
traced the right path or not. So i used this model for
MR with the native data collected in house and i got a
good enough solution. Emboldened i tried my hand at
the native collected at synchroton. This did not give
the solution in P43212/p41212(as suggested by
sytamatic absences) Neither did it give solution in
any of the other P tetragonal spacegroups. I then
tried the mtz file of I4122 and I did get a solution.
What does this suggest? does this mean that my
real space group is I tetragonal
An off origin peak at 1/2 1/2 1/2 may suggest
pseudotranslational symmetry....but ..what if i
process an I tetrgonal as Ptetragonal wont that also
give a peak at 1/2, 1/2, 1/2. How do we distinguish
between these two cases.....
there are certainly certain changes taking place at
the synchroton that make the data collected there to
have an ambiguity with regards to the spacegroups
though the same crystals give umambiguous spacegroup
with data collected in house. What implication these
changes have with regards to the isomorphism of a set
of datasets collected at synchroton. This is because
the same sort of "change" may not occur for different
crystals. I am sayiing this because though i am
observing large differences between the native and
derivatives, i am ending up with bad phasing
statistics with solve and mlphare ( i have tried
p43212, p41212 and i4122)
What else can i do to build up more of my model
(apart from trying to collect another better set of
Thankyou all for your kind attention. Thanks
in advance for all the suggestions.
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