Dear Ewa, I can model a 3 residues sugar chain in the glycosylated protein. The structure was build with an identical 2.3 A resolution structure as model. The final structure is nearly identical with its model. So I think the model is not wrong. The data was collected at 100K. During the refinement, the TLS analysis was included using the program Phenix. By analysis the structure, I found that only the 50 kD protein (the one with lower B factor of 70) contributed to the crystal packing., while the glycosylated 20 kD protein do not paticipate the crystal packing. It is only stablized by the interaction with the large one. I think this will probably explain the extra high B factor of the glycosylated 20 kD protein. Am I right?
Thanks and best wishes. On Fri, Jul 31, 2009 at 12:29 AM, Skrzypczak-Jankun, Ewa < [email protected]> wrote: > all the errors go into B and so you can get decent R with wrong > structure. Glycosylated proteins have a large component totally disordered - > do you see any sugars? > with B~133 you uj is 3.7A which means that atom is all over the place and > meaningless > As a reviewer I would certainly question the interpretation of such > structure. > If the data collection was at 100K (or any cryo condition) one expects B~20 > for a good structure and higher only on the outskirts of the molecule > exposed to solvent where you expect more flexibility and thus disorder, also > in case for flexible loops. But if you have high B for something like a > helice I would suspect a libration movement for the entire helice and you > may refine it with partial occupancy for two positions for example. > Have you done TLS analysis for your complex? > Just a suggestion - TLS is worth looking at and consider including into > refmac for refinement. > E. > > > ________________________________________________________________________________ > > Dr. Ewa Skrzypczak-Jankun Associate Professor > University of Toledo e-mail: > [email protected] > Health Science Campus Mail Stop#1091 > http://golemxiv.dh.meduohio.edu/~ewa<http://golemxiv.dh.meduohio.edu/%7Eewa> > Department of Urology Dowling Hall > r. 2257 > 3000 Arlington Ave. phone 419 > 383 5414 > Toledo OH 43614 fax > 419 383 3785 > > _________________________________________________________________________________ > > > ------------------------------ > *From:* Jiamu Du [mailto:[email protected]] > *Sent:* Thu 7/30/2009 12:15 PM > *To:* Skrzypczak-Jankun, Ewa > *Subject:* Re: [ccp4bb] question of extra high B factor > > Dear Dr. Ewa, > I have checked the data with Phenix. It is not a twin. I think the > spacegroup is right, or else the R/Rf factor should not be so low. > Best wishes. > > On Fri, Jul 31, 2009 at 12:05 AM, Skrzypczak-Jankun, Ewa < > [email protected]> wrote: > >> have you check for twinning? or if the choice of the space group is >> correct? >> take a look at 1LOX and 2P0M in PDB - this is an excellent example of >> simple errors >> Good luck - E. >> >> >> ________________________________________________________________________________ >> >> Dr. Ewa Skrzypczak-Jankun Associate >> Professor >> University of Toledo e-mail: >> [email protected] >> Health Science Campus Mail Stop#1091 >> http://golemxiv.dh.meduohio.edu/~ewa<http://golemxiv.dh.meduohio.edu/%7Eewa> >> Department of Urology Dowling Hall >> r. 2257 >> 3000 Arlington Ave. phone 419 >> 383 5414 >> Toledo OH 43614 fax >> 419 383 3785 >> >> _________________________________________________________________________________ >> >> >> ------------------------------ >> *From:* CCP4 bulletin board on behalf of Jiamu Du >> *Sent:* Thu 7/30/2009 12:00 PM >> *To:* [email protected] >> *Subject:* [ccp4bb] question of extra high B factor >> >> Dear All, >> I am refining a structure of a complex between of 50kD protein and a 20kD >> glycosylated protien. The data is of 2.9 A resolution. The wilson B factor >> is as high as 86.3 A^2. >> The refinement seems well with R/Rf of 0.21/0.25. But the B-factor is >> extra high. For the 50kD part, the average B factor is 76.5 A^2. But the B >> factor of the 20 kD glycosylated protein is as high as 133.3 A^2. Although >> the electron density looks fine, even the sugar chain is seen clearly. >> My question is: >> 1. How to reduce the B factor to a reasonable level? >> 2. If it can not be redueced, when I published it, is this value >> acceptable? >> 3. In the same of similar resolutionIs, is there some other structures >> like this situation? A component or a subunit of the protein has a extra >> high B factor as high as 130. >> >> Thanks and best wishes. >> >> >> -- >> Jiamu Du, Ph.D. >> State Key Laboratory of Molecular Biology >> Institute of Biochemistry and Cell Biology >> Shanghai Institutes for Biological Sciences >> Chinese Academy of Sciences >> 320 Yue-Yang Road >> Shanghai 200031 >> P. R. China >> Tel: +86-21-5492-1117 >> E-mail: [email protected] >> > > > > -- > Jiamu Du, Ph.D. > State Key Laboratory of Molecular Biology > Institute of Biochemistry and Cell Biology > Shanghai Institutes for Biological Sciences > Chinese Academy of Sciences > 320 Yue-Yang Road > Shanghai 200031 > P. R. China > Tel: +86-21-5492-1117 > E-mail: [email protected] > -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yue-Yang Road Shanghai 200031 P. R. China Tel: +86-21-5492-1117 E-mail: [email protected]
