If I go back to my SCALA mtz and run 'Truncate', I get a completely different B value at 27.3, which is obviously much better. However, why did I have to do this, and where would I find this value at the end of my refinement? i.e. did I miss a line in PROCHECK or my final REFMAC log file?
Thank you all, Jim --- On Wed, 8/20/08, Lijun Liu <[EMAIL PROTECTED]> wrote: > From: Lijun Liu <[EMAIL PROTECTED]> > Subject: Re: [ccp4bb] Lower completeness, decent R factors, but low B > factor... > To: [email protected] > Date: Wednesday, August 20, 2008, 1:32 PM > What is the reason for lower completeness is important. > 1) rotation range is not wide enough----you lost frames? > What about > the completeness against > resolution shell? > 2) too many rejections? > a) symmetry error > b) really bad crystal (this seems not the case) > c) too many overlaps during collection, mosaicity .... > Guess 1) is your case, if I can. > > Also, good R factors from low-completeness (either reason > above) is > less reliable. > > Good luck. > > Lijun > > > On Aug 20, 2008, at 9:24 AM, James Pauff wrote: > > > Hello all, thank you for the responses. Just to clear > up a couple > > of things... > > 1) My dataset was acquired on a synchrotron and > scaled/truncated > > there. To my knowledge they used the same procedure > as for other > > structures that we have obtained there...which have > had no B factor > > issues. Granted, our modified protein is of a > different spacegroup > > than previous. > > > > 2) I have not used/touched the TLS parameters at all. > > > > The idea that our 73% completeness (thus lacking 27% > of the > > 'weakest' reflections) has lead to an > artificially low B factor > > sounds most appealing at this point? > > > > As usual, I greatly appreciate all of your insights > here! > > > > Best, > > Jim > > > > > > --- On Wed, 8/20/08, Eleanor Dodson > <[EMAIL PROTECTED]> wrote: > > > >> From: Eleanor Dodson <[EMAIL PROTECTED]> > >> Subject: Re: [ccp4bb] Lower completeness, decent R > factors, but low > >> B factor... > >> To: [EMAIL PROTECTED] > >> Cc: [email protected] > >> Date: Wednesday, August 20, 2008, 4:30 AM > >> James Pauff wrote: > >>> Hello all, > >>> > >>> I have a refined structure at 2.6 angstroms > that at > >> about 73% completeness at this resolution. The > I/sigma is > >> about 2.0 at 2.6 angstroms, and the omit density > for my > >> ligands is great contoured at 3.0sigma. My Rcryst > is 19 or > >> so and the Rfree is 24.5 or so. > >>> > >>> HOWEVER, my mean B value is 13.9, whereas my > other 2 > >> structures (at 2.2 and 2.3 angstroms, same > protein, >95% > >> completeness) have mean B values of 22+. Any > suggestions as > >> to what is going on here? I'm having trouble > explaining > >> this. > >>> > >>> Thank you, > >>> Jim > >>> > >>> > >>> > >>> > >>> > >>> > >> Have you used TLS - listed B factors will then be > given > >> relative to the > >> TLS parameters. You need to run tLSANL to get a > more > >> realistic value. > >> Eleanor > >> > >> > >> But in fact temperature factors are rather harder > to > >> estimate at lower > >> resolutions than higher. Look at your <Fo> > and > >> <Fc> curves v resolution > >> ( part of a REFMAC loggraph) and you can see that > sometimes > >> the overall > >> scaling struggles to get a reasonable fit.. > > > > > > > > Lijun Liu, PhD > Institute of Molecular Biology > HHMI & Department of Physics > University of Oregon > Eugene, OR 97403 > 541-346-4080
