Protein
NMR Structures Refined with Rosetta Have Higher
Accuracy Relative to Corresponding X‑ray Crystal Structures
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Abstract
We
have found that refinement of protein NMR structures using Rosetta
with experimental NMR restraints yields more accurate protein NMR
structures than those that have been deposited in the PDB using standard
refinement protocols. Using 40 pairs of NMR and X-ray crystal structures
determined by the Northeast Structural Genomics Consortium, for proteins
ranging in size from 5–22 kDa, restrained Rosetta refined structures
fit better to the raw experimental data, are in better agreement with
their X-ray counterparts, and have better phasing power compared to
conventionally determined NMR structures. For 37 proteins for which
NMR ensembles were available and which had similar structures in solution
and in the crystal, all of the restrained Rosetta refined NMR structures
were sufficiently accurate to be used for solving the corresponding
X-ray crystal structures by molecular replacement. The protocol for
restrained refinement of protein NMR structures was also compared
with restrained CS-Rosetta calculations. For proteins smaller than
10 kDa, restrained CS-Rosetta, starting from extended conformations,
provides slightly more accurate structures, while for proteins in
the size range of 10–25 kDa the less CPU intensive restrained
Rosetta refinement protocols provided equally or more accurate structures.
The restrained Rosetta protocols described here can improve the accuracy
of protein NMR structures and should find broad and general for studies
of protein structure and function