Hi Fred, On Wed, May 30, 2012 at 08:55:35AM +0200, Vellieux Frederic wrote: > For practical purposes, a "derivative" is considered non isomorphous > when the differences in unit cell parameters exceed ca. 1% (this is > because if you take 2 crystals from the same crystallisation drop > and collect and process diffraction crystals from these 2 crystals, > you will never get exactly the very same values for the unit cell > parameters; non-isomorphism effects start at ca. 1% change and > you'll never get 2 perfectly isomorphous crystals - even if you > collect diffraction data twice from the same crystals you will not > get "perfect isomorphism"). > > From the values mentioned, 1% of the cell parameters of the native > for a and b is 1.81 Angstroem and for c 1.1 Angstroem (the angles do > not matter for a trigonal space group). > > Had you obtained a value for a, b larger than ca. 183 Angstroem, or > below ca. 109.2 Angstroem (only in the direction indicated by the > changes mentioned in your mail - I ignored changes in the opposite > direction) then you would have been able to say that the crystals > were non-isomorphous to each other. For me they are isomorphous to > each other and I ignore these small differences in unit cell > parameters.
I would be careful with the (popular) percentage-rule here: the absolute value of cell differences is much more important. At least if we assume that the change in cell parameters roughly corresponds with a shift in actual atoms. If you have a 1000A cell then a 1% difference could mean a shift of 10A ... clearly, a helix moved 10A away results in something completely different. But with a cell of 20A you could have a 0.2A shift, which you might hardly notice. See eg. 5.2 in Garman & Murray (2003): http://journals.iucr.org/d/issues/2003/11/00/ba5042/index.html which shows 5.2. Non-isomorphism One of the biggest problems of heavy-atom derivatization is that incorporation of a heavy atom into the lattice often induces a change in the unit cell away from the native crystal values, i.e. the derivatized crystal is non-isomorphous to the native crystals. The heavy atom may perturb the arrangement of protein molecules in the crystal or distort the protein molecule, causing a change in unit-cell lengths. Note, however, that it is also possible for the protein to move within the original unit cell (resulting in a different sampling of the molecular transform). The same unit cell is thus a necessary but not sufficient condition for isomorphism. Crick & Magdoff (1956[Crick, F. H. C. & Magdoff, B. S. (1956). Acta Cryst. 9, 901-908.]) calculated that a 0.5 Å change in all three unit-cell edges of a 100 Å cubed unit cell would change the diffraction intensities by an average of 15% in a 3 Å resolution sphere. The predicted intensity changes induced by non-isomorphism increase at higher resolution. When faced with a non-isomorphous derivative, it is the absolute change in the cell which should be considered compared with the working resolution, rather than the relative change, i.e. a change of 1.0% in a 100 Å unit cell edge has a similar effect to that of a 0.5% change in a 200 Å unit cell edge, if compared at similar resolutions. As a general rule of thumb, a change in cell dimensions of dmin/4 is tolerable, where dmin is the resolution limit (Drenth, 1999[Drenth, J. (1999). Principles of Protein X-ray Crystallography, 2nd ed. Berlin: Springer-Verlag.]). For instance, for 2.5 Å data, a 0.6 Å change in the unit cell might be acceptable, whereas at 3.5 Å this could rise to 0.8 Å. Cheers 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) ***************************************************************
