Pavel,
Thanks for the quick response. I just listed out the Fo-Fc column of
the reflection files, and it looks the strongest densities are mostly
along c* and many located in the 2.1A region. I think you may be right.
Lijun
On Jul 20, 2010, at 4:05 PM, Pavel Afonine wrote:
Hi,
It looks like the data is highly anisotropic - I've seen it many
times. You can either apply anisotropy correction (http://www.doe-mbi.ucla.edu/~sawaya/anisoscale/
) or use PHENIX tools to compute the maps - anyone of both should
help. The major difference between the two is that PHENIX will not
modify your original data in any way. Let me if using PHENIX map
calculation tools does not help.
Cheers,
Pavel.
On 7/20/10 3:19 PM, Lijun Liu wrote:
Hi all,
I solved a structure and the refinement is close to complete.
However, some residual density puzzles me.
The SG is P212121, and the c is 84.8 Å. Along c, in several small
but not all regions, there are some layered, alternately appeared
positive and negative residual density pieces (c is the norm of
these plane-like pieces; 3-sigma contour for pos and neg difference
densities). The distance between the neighboring positive pieces
is measured to be ~2.1 Å, corresponding to ~1/40 *c. In one of
such region, there is an indole ring of Trp that is approximately
parallel to the plane-like residual density pieces (attached
figure). In two other regions, there are Leu or else but not ring
structure.
The data is complete to 1.9 Å. Reflection check did not show any
special imcompleteness (ice ring loss, wedge loss, other resolution
bin loss, etc). It looks like to me that there is a systematic
loss of information which made it is specially sensitive to ~2.1 Å
reflections (especially those along c*). It does not look like to
me to be radiation damage. Crystal was needle and showed somehow
polarized (but never serious) diffraction pattern along c*.
Attached is a piece of map with the above-mentioned Trp included.
I would like to know if some one also met something like this
before. Thanks for any comments.
Lijun Liu
Cardiovascular Research Institute
University of California, San Francisco
1700 4th Street, Box 2532
San Francisco, CA 94158
Phone: (415)514-2836
Lijun Liu
Cardiovascular Research Institute
University of California, San Francisco
1700 4th Street, Box 2532
San Francisco, CA 94158
Phone: (415)514-2836