Hmmm - is there a smaller lattice which might fit the density? As Andrew says there are examples of pseudo emptiness in crystals but there are more examples of wrong lattices! Check for non-crystallographic translation? You could attach the pointless/aimless/etc log files.. Eleanor
On Fri, 22 Jul 2022 at 10:15, Andrew Leslie - MRC LMB < and...@mrc-lmb.cam.ac.uk> wrote: > Dear Florian, > > There have been previous examples where there are > distinct “layers” of protein packing without any obvious density linking > the layers, as it appears in the image you show. One is tyrosyl tRNA > synthetase, where the layers were in fact linked by a disordered domain for > which there was no density. Does the density that you see account for the > entire protein (or complex) that you have crystallised? > > I am fairly sure that this has also been seen for membrane proteins, where > the extra-membrane component (or an additional protein, eg a Fab) has been > disordered, again giving layers of density that appear unconnected. > > I’m not sure what you mean by “having two distinct lattices”. Do the > diffraction images show any signs of disorder, eg diffuse streaking or > features that are not accounted for by the lattice used when integrating > the data? > > Best wishes, > > Andrew > > On 21 Jul 2022, at 19:29, Schubot, Florian <fschu...@vt.edu> wrote: > > Hi, I have a high-resolution data set ~1.6 Angst.) for a twinned crystal > (SG C2, twin law h,-k,-l). The structure was solved via molecular > replacement. The map and model look excellent but R and Rfree continue to > hover around 30%. I do use twinned refinement. Reviewing the packing, I > noticed a huge gap between layers (picture below). There is NO additional > well-defined protein density in this gap. I this gap is a symptom of having > two distinct lattices. I was curious if anyone could advise/comment. > Thank you, > Florian > > <image.png> > > ========================================================= > Florian Schubot, Ph.D. > > Associate Professor > Virginia Polytechnic Institute and State University > Department of Biological Sciences > 5002 Derring Hall > 926 West Campus Dr > Blacksburg, VA 24061 > United States > E-mail: fschu...@vt.edu > Phone: (540) 231-2393 > Fax: (540) 231.4043 > http://www.faculty.biol.vt.edu/schubot/ > ========================================================= > > ------------------------------ > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
