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 <[email protected]> >Subject: Re: [ccp4bb] Residual densities! >To: [email protected] > > 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
