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describe its net vibrational displacement[80]. The method is capable of identifying both
large and small vibratory groups, and is largely independent of the resolution of the X-ray
data used to refine the crystal structure. The validity of TLSMD analysis in the context of
crystallographic refinement can easily be judged by tracking the standard crystallographic
residuals R and Rfree resulting from refinement of TLSMD-generated models against the
original diffraction data. In many cases multi-group TLS models are strikingly successful
at predicting the observed diffraction data, and out-perform conventional crystallographic
models during refinement[41, 81]. It is logical to conclude that TLSMD correctly
identifies actual vibrational modes of the protein within the crystal. We are interested to
test the extent to which these same vibrational modes are also present in solution, and the
extent to which the boundaries between vibratory groups identified by TLSMD
correspond to specific hinge points identified by other experimental methods.
TLSMD partitions the protein chain into N segments. It currently has no automated
mechanism for distinguishing segment boundaries that might correspond to inter-domain
hinges from segments boundaries that might, for example, define the endpoints of a
flexible loop. To the extent that it assigns an order of importance to these boundaries, it
does so based on their relative contribution to the observed distribution of atomic
displacements in the crystal structure. Thus TLSMD may identify the boundaries of
highly flexible, albeit small, regions before it identifies those of large domains whose
vibrational amplitude is highly restricted by the crystal lattice. Therefore each segment
boundary, or breakpoint, may possibly correspond to a hinge. But we faced a difficulty in
deciding how many TLSMD breakpoints to compare against the hinge points listed in
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