Thank you all. I think I have know how to deal with this situation. Best Regards.
On 11/1/07, [EMAIL PROTECTED] < [EMAIL PROTECTED]> wrote: > > Dear Jiamu, > This is a matter of debate, but I prefer to publish something as close as > possible to the "true" situation. Publishing a structure with > artificially inflated B-factors is, in my opinion, further from the "truth" > than publishing a structure with an estimated occupancy, even with a > relatively large error, which, by the way, will be less than the error you > create when you let the B-factors soak-up the occupancy problem. > The problem is that occupancy and B-factors are linked at the resolution > you have, so you cannot refine them independently. > You have the following options (decreasingly accurate, but increasingly > easy and robust to implement). > > 1) refine individual B-factors and a group occupancy for the substrate. > Unless the substrate gets cleaved, it will enter or leave the active site as > one piece. If it does get cleaved, you could try to refine group occupancies > for the two parts as the would be formed after cleavage. > > 2) fix the B-factors of the substrate to those of the surrounding protein > and refine a (group)occupancy, but no B-factors. (if you can refine > B-factors, you can refine occupancies with similar accuracy, but you can not > refine the two at the same time). Then fix the occupancy of the substrate to > the refined value (if you used individual occupancies, you have to take the > average value) and do another round of B-factor refinement. > > 3) run several refinement trials with different fixed occupancy, say 0.3, > 0.4, 0.5 etc. Steps of 0.1 are more than fine enough. Say with value > results in R-factors in the range of the surrounding protein. > > Again, I would advice against publishing a structure with B-factors you > are sure they are wrong. > Herman > > ------------------------------ > *From:* Jiamu Du [mailto:[EMAIL PROTECTED] > *Sent:* Thursday, November 01, 2007 1:23 PM > *To:* Schreuder, Herman SMA/DE > *Cc:* ccp4bb@jiscmail.ac.uk > *Subject:* Re: [ccp4bb] the B facot of soaked substrate > > > Dear Herman: > It is due to the occupancy obviously. > Previously, someone mensioned that in this resolution it is not suitable > to refine the occupancy. > So I think it is better for me to keep the occupancy to 1. > Do you have some case for this situation in the PDB bank? > > Thanks. > > > On 11/1/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> > wrote: > > > > Deart Jamu, > > You probably do not have full occupancy. Set the occupancy of the > > inhibitor to say 0.6 and refine again and see what happens to the > > B-factors. > > Herman > > > > ** > > ------------------------------ > > *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of > > *Jiamu Du > > *Sent:* Thursday, November 01, 2007 1:05 PM > > *To:* CCP4BB@JISCMAIL.AC.UK > > *Subject:* [ccp4bb] the B facot of soaked substrate > > > > > > Dear All: > > I am refining a protein structure with a soaked substrate. > > The resolution is 2.5 A. The B factor of protein is around 40, while the > > B factor of the soaked substrate is as high as 80. > > The density looks fine. > > Is this structure acceptable? Or is there anyone who can give me an > > example of this situation in the PDB bank? > > Thanks. > > > > > > -- > > Jiamu Du > > State Key Laboratory of Molecular Biology > > Institute of Biochemistry and Cell Biology Shanghai Institutes for > > Biological Sciences > > Chinese Academy of Sciences (CAS) > > > > > > -- > Jiamu Du > State Key Laboratory of Molecular Biology > Institute of Biochemistry and Cell Biology Shanghai Institutes for > Biological Sciences > Chinese Academy of Sciences (CAS) > -- Jiamu Du State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS)
