Dear alphar~
... I guess that a lot of the subsequent advice depends to the counter-
question "Which program did you use for phasing "?
My view on the subject is summarized in:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Experimental_phasing
[any contributions are welcome to it o sit can become less of my view
and more representative]
~/A.
On Feb 21, 2009, at 4:11, 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~
:)
P please don't print this e-mail unless you really need to
Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
Department of Biochemistry (B8)
Netherlands Cancer Institute,
Dept. B8, 1066 CX Amsterdam, The Netherlands
Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
