Re: [ccp4bb]: Alternate side chains..

[Daniel Anderson <dha@mbi.ucla.edu>]

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Hello all.

Building alternate conformations can make a noticeable difference
in the global statistics R and Rfree when the discretely disordered
side chains are a large fraction of the structure.

The examples that I know about are both 12-mer peptide structures,
1BYZ and 3AL1:

Packed Protein Bilayers in
the 0.90A Resolution Structure of a Designed Alpha Helical Bundle.
Gilbert Prive, Daniel H. Anderson, Laura Wesson, Duilio Cascio,
and David Eisenberg.
Protein Science (1999), 8, 1400-1409.

Centrosymmetric Bilayers in the 0.75A Resolution Structure of a
Designed Alpha-helical Peptide, D,L-Alpha-1.
William R. Patterson, Daniel H. Anderson, William F. DeGrado,
Duilio Cascio, and David Eisenberg.
Protein Science (1999), 8, 1410-1422.

In Prive, et al, I think the single-conformation model had
Rfactor about 0.1 or a little more,
while the "final" model with split side chains had Rfactor= 0.086 .
In Patterson, et al, Table 5, model r8 was the last with single
conformations, with Rfactor= 0.213 . The "final" model with almost all
side chains split had Rfactor= 0.131 .

My recollection is that the most important thing I did in
finalizing those two refinements was to model the multiple conformations.
In the centrosymmetric case, increasing the number of significant digits
in the intensity numbers also made an emarrasingly large improvement,
so the difference due to the disorder model was a little less than
0.213-0.131 .


* Daniel Anderson, Ph.D.                   *
*                                          *
* Howard Hughes Medical Institute          *
*   and                                    *
* DOE-Molecular Biology Institute          *
* Paul Boyer Hall room 219                 *
* University of California at Los Angeles  *
* Los Angeles, CA 90095-1570               *
* USA                                      *
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On Wed, 4 Dec 2002, raji wrote:

> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
> Hi,
> Have people seen an improvement in R-factor and R-free following addition of
> alternate sidechains to their structures ?
> Could you pl. share your experience since I dont see any change and I wonder
> what's going on.
> Thanks,
> Raji
>
> Rajeswari Edayathumangalam
> Dept. of Biochemistry & Molecular Biology
> Colorado State University
> Fort Collins, CO 80523 USA
>