Hi All,
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
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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
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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
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