RE: [ccp4bb]: Questions about translational NCS

["Rizkallah, PJ (Pierre)" <P.J.Rizkallah@dl.ac.uk>]

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Hi There,

I had a structure with pure translational ncs, which I am still writing up.
It is another version of a structure in a smaller cell. The samller cell had
one layer of the protein, which agrregates in tetramers with 222 particle
symmetry, and the 222 axes are crystallographic (orthorhombic space group,
one molecule in the a.u.). So luckily it was not a complicated case of
n-fold ncs like the general case discussed by Randy Read. The larger cell
was an exact doubling of the smaller cell in the direction normal to the
layer. It so happens that the duplicate is shifted in the plane normal to
the stacking direction by 2.7A, a slippage if you want. That was all the
difference between this and an exact duplication of the smaller cell.

While I did not study the native Patterson, my observation of the intensity
distributions is that the effect was opposite to twinning, like Randy Read
said. It is not difficult to see why, since the ALMOST exact duplication
caused some layers to be weak. So the N(z) plot in TRUNCATE showed a
distribution over to the left of the theoretical, which means the data were
weaker than the symmetry of the cell suggests. Twinning enhances some
reflections so you get the observed distribution to the right of the
theoretical curve.

How to progress with this? I had the model of the protein in the smaller
cell, and I used it for MR. There was one clear rotation solution, which
corresponded with a good translation solution. Fixing this and looking for a
second molecule gave a solution only with the same rotation solution, which
was 1/2 a unit-cell away in the stacking direction, and 2.7A offset in the
plane normal. Even after refining the two MR solutions, there was only
translational ncs between them, within the accuracy of the 1.7A resolution
of the data. Parameters from the fitting step of AMORE were:
             alpha      beta      gamma      Tx        Ty        Tz
Solution 1   63.33     60.59     279.65    0.3546    0.3719    0.3354
Solution 2   62.82     60.68     280.99    0.3566    0.3452    0.8383

The rest of the structure refinement proceeded as normal.

I hope you find this helpful.


Pierre Rizkallah

-----Original Message-----
From: Jianghai Zhu [mailto:zhu5@purdue.edu]
Sent: 20 February 2003 02:16
To: ccp4bb@dl.ac.uk
Subject: [ccp4bb]: Questions about translational NCS


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Hi, all,

I have several questions about translational NCS. 

1) If I have a pure translational NCS, I can find a peak in my 
native patterson map. But if I have a NCS happen to be parallel 
to my crystallographic symmetry, they generate some 
translational vectors and I can find a peak in my native 
patterson map too. How do I know it is a pure translational NCS 
or a NCS parallel to the crystallographic symmetry?

2) I was told that the translational NCS could make the data 
look like a data from a twinning crystal. Is that true? If it 
is, could somebody explain it to me or point out some 
reference? Will the pure translational NCS and NCS parallel to 
crystallographic symmetry give the similar intensity 
distribution? 

Thanks.

Jianghai
-- 
===========================
Jianghai Zhu
Biochemistry & Molecular Biology
Purdue University
Tel: 765-4949249 (O)
      765-4633336 (H)
===========================