Hi alphar~
Check the sites you get from anomalous difference Fouriers and stick
to those as your correct HA sites. At the same time you may consider
not to refine the HA substructure on the anomalous differences but
merely using the isomorphous differences. Maybe you need to change the
scale of your data intensities by a factor 2-3 to get the major sites
at an occupancy of ~1 in the SIR/MIR refinement.
Finally R32/R3 space groups are prone to twinning problems in which
case the MIRAS phasing will be a nightmare explaining your current
pathologies
Poul
On 21/02/2009, at 04.11, Fengyun Ni wrote:
Hi everyone!
I have a question on my poor MIR map.
Four datasets (two AU and two HG) were used for phasing upto 3 A
resolution in my case. I could locate several heavy atom sites for
each dataset with occupancy finally refined to about 0.3 to 0.4, and
with B value refined to about 50 to 80. I did not include the
anomalous data because once I refine against anomalous data, the
anomalous occupancy was only about 0.02, and even smaller as 0.004
for some sites. I guess the anomalous data are not good enough, so I
did not use them right now (Could I do this? Or must I include them
somehow?).
The FOM I got is about 0.6, the Cullis-R factors were about 0.6 for
all four data sets, and the phasing power was about 2.5 in each
dataset. After I did the density modification, the FOM could increas
to about 0.8.
My problem is that the protein should form a long helix structure as
indicated by other homology protein, but in the map after density
modification, the densities are not consecutive though the overall
shape seemed to be a long helix. The good thing is that some short
helix-like densities could be observed in the current map, but they
are not connected to each other.
Right now, I am totally lost whether I should believe in the mir-map
I have. Could I improve this map with some other method? Or should I
re-do the phasing?
BTW, the space group for my crystal is R3 or R32 with a=50, b=50,
c=380, alpha=90, beta=90 and gamma=120. The c-axis is much longer
than a- and b-axis, so the reflection data suffered from the
anisotroy effect.
Any suggestion on my phasing problem is welcome.
--
Alphar Ni
Call me alphar~
:)
