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Re: [ccp4bb] B-factor & Space gr questions! |
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CCP4bb navigationCCP4bb <-- 2007 <-- June 2007 <-- 05 June 2007Subject: Re: B-factor & Space gr questions! From: "Ibrahim M {- dot -} Moustafa" I {- dot -} moustafa {- at -} PSU {- dot -} EDU Date: 2007-06-05 Thanks a lot for all reply with valuable inputs. In my original post: I meant a = b "does not equal" c. I used # for "does not equal". Many asked where is that paper published! Actually the paper is under revision. When reading, I assumed the unit cell dimensions (or the space group) is a typo as others thought. The low B value for the low resolution structure makes me suspicious that something is wrong. In my little experience, and as others mentioned, B-factor is expected to be around 70-80 for 2.8 A structure and very likely higher for 3.0 A structure. David Briggs suggested that they reported the Wilson B-factor; however, clearly, it is reported as the B-factor of the refined structure. Also, the Rwork = Rfree indicated that something is not right with the refinement protocol but I was not sure what that could be! The suspect that they did not transfer the FreeR sounds reasonable explanation. thanks a lot, Ibrahim At 03:50 AM 6/5/2007, Eleanor Dodson wrote: >Yes; a==b for P6i - prob. a typo.. > >B factors at 3.2A are hard to fix - it will depend on scaling >convention to some extent.. >Can you download the data and re-run refinement for your own satisfaction. > >If R ==Rfree for the complex then I suspect they did not transfer >the FreeR flags from the apo-protein data to the complex. >Again if the data is available you may be able to check this. >Eleanor > > > >Ibrahim M. Moustafa wrote: >>Hi all, >> >> While reading a crystallographic paper describing the structure >> of an apo-protein and its complex I noticed that >> >> the authors described the space goup as P6122 for the unit cell: >> a=141.9, b=143.9, c=380.4 ! >> >> Could this be considered as a typo or I'm missing something here! >> the requirement for the hexagonal is a = b # C....right? >> >>Another observation in that paper too: the B-factors for the 2.4 A >>and 3.2 A structures are 39 and 40?? Does this make sense to anyone?? >> >>The last question: In the same paper, for the complex structure R >>and Rfree are equal (30%) is that an indication for improper >>refinement in these published structure? I'd love to hear your >>comments on that too. >> >> thanks, >> Ibrahim >> >> >> >> >>---------------------------------------------------------------------------------------------------------- >> >>Ibrahim M. Moustafa, Ph.D. >>Biochemistry and Molecular Biology Dept. >>201 Althouse Lab., Uinversity Park >>Pennsylvania State University, PA16802 >> >>Tel. (814)863-8703 >>Fax. (814)865-7927 >>---------------------------------------------------------------------------------------------------------- >> >> ---------------------------------------------------------------------------------------------------------- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park Pennsylvania State University, PA16802 Tel. (814)863-8703 Fax. (814)865-7927 ---------------------------------------------------------------------------------------------------------- CCP4bb navigationCCP4bb <-- 2007 <-- June 2007 <-- 05 June 2007 |
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