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On Wednesday 13 May 2009 10:31:50 Jacob Keller wrote: > So what is the approximate percent contribution of the > *temperature-dependent* b-factor at 100K, for an average crystal, or how to > determine such? I gave a reference for how to determine this. But as I said, to the best of my knowledge the experiment has never been done for a protein structure. And even if it has been done for some small number of cases, I am leery of extrapolating to an "average crystal". > In other words, if I have a crystal with an avg B of 20, > when I go from 100K to 0K, how much lower will it drop? I recall seeing > papers exploring liquid helium temperatures, which I believe concluded that > there was not much gain in lowering the temp, implying that the B's did not > go down much after 100K. I think the "not much gain" conclusion from liquid helium experiments was with regard to radiation damage, not B factors. Do you really care what the ADPs are, so long as they accurately describe what is in your crystal? Ethan > I had thought that the reason for calling it a temperature factor was more > because it represented the many states of the atoms caught *in flagrante > vibratio* by the liquid nitrogen plunge upon freezing the crystal, but not > actual motions in the crystal. Room temperature is of course different. > > Jacob > > ******************************************* > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > Dallos Laboratory > F. Searle 1-240 > 2240 Campus Drive > Evanston IL 60208 > lab: 847.491.2438 > cel: 773.608.9185 > email: [log in to unmask] > ******************************************* > > ----- Original Message ----- > From: "Ethan Merritt" <[log in to unmask]> > To: <[log in to unmask]> > Sent: Wednesday, May 13, 2009 12:12 PM > Subject: Re: [ccp4bb] phasing with se-met at low resolution > > > On Wednesday 13 May 2009 09:30:06 Jacob Keller wrote: > > > The reason is that you've missed out one important term: the atomic > > > displacement parameters (B-factors), which describe a combination of > > > thermal motion and positional disorder between unit cells. > > > > A somewhat niggling point: isn't it true that the thermal motion is > > insignificant at 100K? > > No. True thermal motion doesn't bottom out until 0 Kelvin. > But that is kind of irrelevant, since "motion" in the sense of > "things moving in the crystal while we measured the data" is only > one contribution to the overall ADP (B factor). > > > > Does anybody know of a paper which systematically > > measures B-factors as a function of temperature? The asymptote of the > > resulting curve would represent all of the non-thermal elements, right? > > The theory for this is well laid out in > > Bürgi, H.B., and Förtsch, M. (1999). > Dynamic processes and disorder in crystal structures as seen by > temperature-dependent diffraction experiments. > J. Molecular Structure 486, 457-463. > > But to the best of my knowledge a full analysis based on > temperature-dependent diffraction experiments has never been done for a > protein structure. I had a preliminary go at it some years back, but > collecting comparable data sets over a range of temperatures spanning > liquid He to room temperature is technically challenging. The analysis > is also non-trivial. > > > -- > Ethan A Merritt > Biomolecular Structure Center > University of Washington, Seattle 98195-7742 > > > -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742