It is pretty hard to decide on a space group when you have NC
translation 1/2,1/2,1/2.
All h00 0k0 and 00l odd reflections will be weak
But here is one solution..
If you assume 2 molecules seperated by 1/2,1/2,1/2
Take your "harker" vector as 0.1712 0.5000 0.1674, then you would
have an anom scatterer at
0.086, 0, 0.0837 fixing the y coordinate at 0. The symmetry equivalent
is -0.086 0.5 -0.0837
Then the translation gives you another site at 0.586 0.5 0.5837 and
-0.586 0.0 -0.5837 with the same Harker vector
And the vector between -0.086 0.5 -0.0837 and 0.586 0.5 0.5837 is
0.6712, 0.0, 0.6674 equivalent to 0.3288 0 0. 333 - your peak 3
The peak heights look rather peculiar though..
And yes - you can use an anom scatterer for phasing without knowing its
atom type - the maths are more or less identical for any scatter..
Eleanor
er
Hay Dvir wrote:
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Hello All,
I collected a putative 'Native' data set which processes best as
primitive monoclinic. Although the beta angle is ~91 degrees the data
wouldn't scale well as orthorhombic. The native patterson suggest
translation NCS, while the anomalous difference Patterson indicates
the presence of an anomalously scattering atom/s.
Since the peaks between the two maps are related (see below) and in a
'simplified thinking' suggest that the anomalous scatterer/s each
correspond to a different NCS entity. However, NCS translation of
exactly half the unit cell seems a bit suspicious. Moreover, the
translation peak (at v=0.5) suggest p21, while the anomalous
difference peak shows up at v=0.0 suggesting p2.
On the native Patterson I get a strong (2/5 of the origin) centering
peak (second) at the v=0.5 section:
GRID 60 36 84
CELL 80.0253 48.1743 113.8849 90.0000 90.8015 90.0000
ATOM1 Ano 0.0000 0.0000 0.0000 54.18 0.0 BFAC 20.0
ATOM2 Ano 0.5000 0.5000 0.5000 20.91 0.0 BFAC 20.0
ATOM3 Ano 0.3430 0.0000 0.3424 6.62 0.0 BFAC 20.0
ATOM4 Ano 0.1567 0.5000 0.1592 5.36 0.0 BFAC 20.0
ATOM5 Ano 0.3292 0.5000 0.5088 3.13 0.0 BFAC 20.0
The anomalous difference Patterson for that data shows virtually the
same second and third peaks:
GRID 60 36 84
CELL 80.0253 48.1743 113.8849 90.0000 90.8015 90.0000
ATOM1 Ano 0.0000 0.0000 0.0000 37.37 0.0 BFAC 20.0
ATOM2 Ano 0.5000 0.5000 0.5000 11.73 0.0 BFAC 20.0
ATOM3 Ano 0.3364 0.0000 0.3361 11.44 0.0 BFAC 20.0
ATOM4 Ano 0.1712 0.5000 0.1674 5.43 0.0 BFAC 20.0
ATOM5 Ano 0.1895 0.0000 0.1279 3.63 0.0 BFAC 20.0
ATOM6 Ano 0.0871 0.5000 0.3585 3.51 0.0 BFAC 20.0
What is it that I'm missing?
If indeed, there is an unknown anomalous scatterer can I use it for
phasing without any knowledge of its scattering factors?
Any help would be greatly appreciated!
Thanks, Hay.
==================================
Hay Dvir, Ph.D.
Structural Biology Laboratory
The Salk Institute for Biological Sciences
10010 North Torrey Pines Road
La Jolla, CA 92037 USA
==================================
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