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Hi Marcus,
Do you mean "waters" other than in clathrates ?
Your MS issue is infortunately no longer available at my institution.
Nadir
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Pr. Nadir T. Mrabet
Cellular & Molecular Biochemistry
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Marcus David Collins wrote:
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I hate to toot my own horn, but it *could* be water. See:
Collins et al, PNAS, 102:16668
Non specificly bound water can appear to be smeared out, and water does
not need to be specifically bound in order to appear in hydrophobic cores.
Marcus Collins
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Marcus D. Collins
Gruner Biophysics Group, Cornell University Dept. of Physics, LASSP
(h) 607.347.4720 (w) 607.255.8678 (c) 607.351.8650
"You have opened a new door, and I share this with you,
for I have been where you are now."
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On Thu, 8 Dec 2005, Andrew Wong wrote:
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Hi
Understood and agree. Perhaps my wordings in the original post can be a
bit better.
Perhaps I should ask what have others *found* to be inside the hydrophobic
core/region :) Anyway, in one of the structures I'm working on, there'r 2
(identical) hydrophobic cores, generated by 2mol/ASU (not NCS-averaged,
yet). Each core has 2 blobs of stray density, all appear to have the same
shape. They can't be H2O, neither shape nor size fit, but yet seems abit
too small for MES (in the condition). Just curious what they are, that's
all. It's a 1.6A data set.
Anastassis Perrakis: "...'better modelling' not 'better R'.."
Ok yes, better modelling :) Thanks
Andrew
--------------------
PhD Student
Dept of Biochemistry
Queen's University
Kingston ON Canada
On Thu, 8 Dec 2005, Dirk Kostrewa wrote:
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Dear Lynn Ten Eyck,
I fully agree with you and post this reply only because of the students
that are new to crystallography. Even interpretation of the electron
density of the chemically well known protein polypeptide chain has a
wide grey area: surface side chains, flexible loops and termini,
alternate conformations, etc. (you all know that, of course!).
Interpretation of waters, ions, or any other compounds from the
crystallization buffer is even more fuzzy. But I agree with you, that
one should try the best to get both a physically and chemically
reasonable model. I must admit, however, that even with a well-refined
protein with, say, 2 A with R/Free-R ~ 15/19% and good stereochemistry,
I still have the feeling that there are errors that I didn't
detect/correct, and this is certainly true. As in the saying " . . .
protein refinement is never finished but aborted . . ." (was it you,
Phil, who said that?)
Best regards,
Dirk.
Lynn Ten Eyck wrote:
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Please do *NOT* just add what are essentially content-free dummy atoms
just to lower the R. This just adds extra parameters to soak up
potentially valuable information about the quality of the structure.
The real refinement problem is to find a physically plausible model
that, properly adjusted, fits the data to within the experimental error
of the data. Uninterpreted blobs are not a molecular model. If you DO
put a molecular component on that density, you are in effect saying "I
really believe, just as strongly as I believe the conformation of the
main chain, that this density is (say) an acetate ion." Do you? If so,
put it in, but you have actual chemical evidence for the composition of
the protein chain.
Best regards,
Lynn Ten Eyck
--
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Dirk Kostrewa
Paul Scherrer Institut
Life Sciences, OFLC/110
CH-5232 Villigen PSI, Switzerland
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E-mail: [EMAIL PROTECTED]
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