Hi, I am refining two crystal structures of the same protein wtih four domains and 687 amino acids. These are the last lines form my log-files after several model building steps - protein altogether fits quite well into the density. But I am confused about these logfiles: 1.Why is there such a big difference between R values with and without bulk solvent correction and anisotropic scale? Start R-work = 0.3765, R-free = 0.5498 (no bulk solvent and anisotropic scale) Final R-work = 0.3733, R-free = 0.5509 (no bulk solvent and anisotropic scale) Start R-work = 0.2356, R-free = 0.2962 Final R-work = 0.2250, R-free = 0.2939 2. (the other structure) Why does the R value without bulk solvent and anisotropic scale decrease so much but with it remains stable? Start R-work = 0.2182, R-free = 0.2856 (no bulk solvent and anisotropic scale) Final R-work = 0.4054, R-free = 0.4223 (no bulk solvent and anisotropic scale) Start R-work = 0.2157, R-free = 0.2827 Final R-work = 0.2147, R-free = 0.2816 I would be very pleased about any helpful comments. Ina Ina Lindemann Philipps-Universität Marburg Pharmazeutische Chemie AG Klebe Marbacher Weg 6 35032 Marburg Tel.: 06421/2825908
On Thu, Mar 31, 2011 at 7:27 AM, Ina Lindemann
1.Why is there such a big difference between R values with and without bulk solvent correction and anisotropic scale?
Start R-work = 0.3765, R-free = 0.5498 (no bulk solvent and anisotropic scale) Final R-work = 0.3733, R-free = 0.5509 (no bulk solvent and anisotropic scale)
Start R-work = 0.2356, R-free = 0.2962 Final R-work = 0.2250, R-free = 0.2939
This is normal - the bulk solvent effect dominates at low resolution, where the amplitudes are largest and thus contribute the most to the R-factors. If you were to turn off bulk solvent correction and truncate your data at 8A or 6A, the gap will mostly disappear. (Don't actually do this, of course, but it appears to have been common practice until around the mid-1990s.)
2. (the other structure) Why does the R value without bulk solvent and anisotropic scale decrease so much but with it remains stable?
Start R-work = 0.2182, R-free = 0.2856 (no bulk solvent and anisotropic scale) Final R-work = 0.4054, R-free = 0.4223 (no bulk solvent and anisotropic scale)
Start R-work = 0.2157, R-free = 0.2827 Final R-work = 0.2147, R-free = 0.2816
Did you mean "increase", or is that first set of numbers backwards? I'm not sure what the explanation is, but I'd advise against worrying too much about the meaning of the unscaled R-factors. (It may not be a good idea for us to display them - it seems to create a lot of confusion, especially since no other refinement program that I've used does this.) -Nat
participants (2)
-
Ina Lindemann -
Nathaniel Echols