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Re: [ccp4bb]: spacegroup problem
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Well, you clearly have pseudo body centering. The question is if you
start out with true body centering which breaks down to a pseudo
centering due to radiation damage or if you had pseudo centering all the
time but just don't realize it in every case. To tell the difference,
index in the primitive setting and look at early diffraction images and
late images. If half of your predicted spots on the early images are
virtually absent but this effect is much less pronounced on the later
images than the pseudocentering is apparently induced by radiation or
other effects at the synchrotron. If this is not the case look at your
in-house data and see if the body-centered indexing solution really
predicts the observed spots (probably easiest to see at lower
resolution). Perhaps you have just not realized they are there until
because the diffraction is so much weaker than at the synchrotron.
Bart
sameeta bilgrami wrote:
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>
> dear all,
> hello,
> 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
> derivatives)
> Thankyou all for your kind attention. Thanks
> in advance for all the suggestions.
> Yours sincerely,
> Sameeta Bilgrami
>
>
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--
==============================================================================
Bart Hazes (Assistant Professor)
Dept. of Medical Microbiology & Immunology
University of Alberta
1-41 Medical Sciences Building
Edmonton, Alberta
Canada, T6G 2H7
phone: 1-780-492-0042
fax: 1-780-492-7521
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