[phenixbb] TLS and ligand question
Andy Torelli
att29 at cornell.edu
Wed Nov 25 10:19:33 PST 2009
To the Phenixbb community:
I've been experimenting with using TLS to refine my 2.4 angstrom
resolution structure. There are 2 protomers in the ASU, and each has a
metal cluster and a small-molecule ligand. The model has a relatively
high average B-factor for protein (~65) atoms and I also suspect that
both the cluster and the ligand have partial occupancy. At this
resolution however, I've modeled both groups with 100% occupancy and the
average B-factors for the atoms of these groups are expectedly higher,
~100 after individual_sites and individual_adp refinement (i.e. no TLS).
My problem arises when I try to use TLS. I determined the boundaries
for the TLS groups using the TLSMD server, which identified 3 groups per
protomer (roughly coincide with domain boundaries). After including TLS
refinement, the R and R-free both improve by 1-2%, but the B-factors for
the clusters and ligands end up very high. Metal atoms in the cluster
have B-factors >350 and the ligand atoms have B-factors >120. The
average B-factor for protein atoms is slightly higher too (~70). Also,
the gap between R and Rfree is larger than I'd expect (19% R and 26%
Rfree), although this isn't unheard of and more importantly, the values
have fully converged yet.
So, should I be treating the ligands differently if I intend to use
TLS? I tried including them with one of the TLS groups, but that didn't
help. Any other ideas are welcome.
Best Regards,
-Andy Torelli
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