Could any of those strong spots at 2.1 be ice?
---- Original message ----
>Date: Tue, 20 Jul 2010 16:13:31 -0700
>From: Lijun Liu <[log in to unmask]>
>Subject: Re: [ccp4bb] Residual densities!
>To: [log in to unmask]
>
> 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
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