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
