In our hands the Rsymm difference after scaling was 3% and the crystals were not particularly isomorphous (1.2 degree difference in beta angle). We were also shooting at room temp and still found a solution. We were using an in house source to optimize the anomalous signal, so if the data was shot at a synchrotron the signal won't be as strong.
To comment on Artem's reply the I3C from Hampton is prepared in LiOH (for solubility purposes) so it is basic already. Our crystallization conditions were at pH 3 and there was no reactivity issue. If you are interested here's the reference. http://www.ncbi.nlm.nih.gov/pubmed/19020356 Cheers, Katherine On Sat, Jan 1, 2011 at 11:55 PM, Artem Evdokimov <artem.evdoki...@gmail.com>wrote: > http://shelx.uni-ac.gwdg.de/~tbeck/papers/mad_triangle.pdf<http://shelx.uni-ac.gwdg.de/%7Etbeck/papers/mad_triangle.pdf> > > is the paper where the 'I3C' designation originates. I also recommend > Dauter's papers on halide phasing - very instructive stuff there. > > 5-Amino-2,4,6-triiodoisophthalic acid as such is not supposed to be > chemically reactive under 'normal' aqueous conditions. This is not to say > that this compound can't react chemically, but I don't expect it to > form/break covalent bonds unless there are chemical activators present > (under right conditions, certain soluble carbodiimides for example may > conjugate this compound to amines such as lysines or the N-terminus of the > protein - although the bulky iodine may hinder the reaction considerably). > So, in strict terms the actual chemical reactivity of this stuff is low. > > I suspect however that you're not really interested in reactivity as such > but rather in the ability of this compound to form loosely associated (but > fairly specific) protein-compound complexes. This is highly dependent on the > nature of the protein you're working with and more specifically on the > availablilty of appropriately shaped and charged zones on the surface(s) > presented by packed protein molecules in your crystals. The answer to this > question in your specific context is 'maybe' - sorry, it's just not very > certain and there's not enough data available on I3C phasing so far to make > a better guess. I hazard to suggest that this stuff will work less well at > basic-ish pH but that's entirely speculative. > > The answer to your second question depends on the nature of your protein > and the crystal, as well as the processing software and specific processing > parameter values employed. Expected contribution (deltaFanom /F ratio) can > be estimated using Hendrickson & Teeter (? or was it earlier than them, so > sorry if it's someone else's) formula which works well for reasonably strong > data (i.e. at low-ish resolutions where measured errors in the data do not > significantly affect the ratio) - but you need to know how many anomalous > scatterers you might expect to find. It's so much easier to collect data > and calculate an anomalous Patterson map, or run some rudimentary phasing > attempts. Several programs output statistics (SHELX package and SOLVE come > to mind) that are also quite useful. > > So, I would recommend that you 'start working on the data' rather than > wonder if it's worth the effort. It's the only way to be sure, and it's not > like it's usually very hard to do a few quick calculations and find out. You > might have a structure in there already. > > Artem > > On Sat, Jan 1, 2011 at 10:10 PM, Vijay Pagadala > <pagada...@niehs.nih.gov>wrote: > >> Hi savers, >> >> What is the reactivity of the I3C compound- Iodine compound for phasing >> from Hampton Research? >> I was wondering if there is any chance that the crystals soaked at 50mM in >> the drop for 24 hours at 4 celcius would stay unreacted to the compound >> I3C. >> Another detail question-How much of a difference in R-factor value after >> scaling (normal Vs anamolous ) is significant to say that there is signal >> from Iodine? >> I know it can be found out after phasing but want to have an idea to even >> start working on the data. >> >> Thanks in advance. >> >> Vijay >> > >
