Guangyu Zhu wrote: > Zn and Se have similar f' and f''. Why Zn seems have much better phasing > powder in practice? Is it just because Zn always binds tightly on protein > but Se might have higher b-factor?
I don't have a better explanation than tighter binding for Zn, although I suppose that it's possible partial Se incorporation could be a factor as well. > > Guangyu > > > On 5/14/09 2:31 PM, "Pete Meyer" <pame...@mcw.edu> wrote: > >> You might find Structure 14, 973-982 Jun 2006 of interest. >> >> Larger protein, Zn instead of Se (although only 8 sites), roughly >> comparable to slightly lower resolution. This was mainly testing to >> confirm that there was enough anomalous signal to phase off of, so the >> model was essentially known; however 50% completeness was enough to >> allow for site location by anomalous or dispersive difference fourier >> (which one sticking point...even if the MR hits don't give a helpful >> model phased map, they can still be good enough for site location). >> >> Pete >> >> Clemens Grimm wrote: >>> OK, here's a concrete case: >>> >>> A 150kDa protein complex, the plate-like crystals can be produced in >>> sufficient number; Se-Met derivatives available, total number of Met >>> around 20, subunits could be marked and combined individually. >>> Diffraction is highly anisotropic, in certain directions up to >>> 3.8A,while in others only 5A. Similarly, the spot quality is very >>> dependent on orientation. >>> Space group I222, a=75 b=150 c=250. Datsets scale well with 3-4% Rsym >>> up to 12 A resolution. At 4.5A Rsym rises above 50% (I/sigma is still at >>> 2.0). The 'sweet' slices of the dataset scale significantly better, but >>> give only 70% (non-anomalous) completness. We hope to improve datasets >>> slightly by orienting the crystals. >>> 65% of the structure would be available as coordinate building blocks >>> from the PDB, however, MR with these components so far did not yield a >>> clear solution. >>> >>> Any suggestions or experiences with similar cases are welcome. >>> >>> Cheers, >>> Clemens >>> >>> Zitat von Clemens Vonrhein <vonrh...@globalphasing.com>: >>> >>> >>> [Show Quoted Text - 64 lines][Zitattext verstecken] >>> Hi Clemens, >>> >>> maybe re-phrasing your question: >>> >>> What would be the best technique/strategy to phase crystals that >>> >>> [ ] diffract to maximal ___ A >>> [ ] typical diffraction to __ A >>> [ ] are radiation sensitive >>> [ ] easily reproducable >>> [ ] large crystals (up to ___ um) >>> [ ] long needles >>> [ ] thin plates >>> [ ] have ___ mol/asu >>> [ ] spacegroup ___ >>> [ ] nice diffraction pattern >>> [ ] poor diffraction pattern (reason: ___) >>> [ ] anisotropic diffraction (resolution in poorest direction: ___ A) >>> [ ] cell dimensions of roughly ___ ___ ___ ___ ___ ___ >>> [ ] purified from native source >>> [ ] expressed in expression system ___ >>> [ ] anything else: _______ >>> >>> Tick the appropriate boxes and fill out the blanks as much as possible >>> - that should give more important and necessary information. There are >>> consequences to consider for all of those points that would then give >>> some rough guidelines for your particular project/problem. >>> >>> Maybe CCP4 should have an online form to describe a particular >>> crystallographic problem? >>> >>> Cheers >>> >>> Clemens >>> >>> On Thu, May 14, 2009 at 09:35:28AM +0200, Clemens Grimm wrote: >>> >>> Dear all, >>> >>> after the SeMet phasing discussion, what would be -in general- the best >>> technique to phase low resolution data (<=4A) of large complexes (>=150 >>> kDA) - in terms of >>> >>> - derivatization compounds (is there something like the 'golden five' HA >>> compounds for these cases), >>> >>> - data collection techniques and >>> >>> - phasing methods? >>> >>> Clemens >>> >>> -- >>> >>> *************************************************************** >>> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com >>> * >>> * Global Phasing Ltd. >>> * Sheraton House, Castle Park >>> * Cambridge CB3 0AX, UK >>> *-------------------------------------------------------------- >>> * BUSTER Development Group (http://www.globalphasing.com) >>> *************************************************************** >
