Abstract
Accurate geometric restraints are vital in the automation of macromolecular crystallographic structure refinement. A set of restraints for the Fe4S4 cubane-type cluster was created using the Cambridge Structural Database (CSD) and high-resolution structures from the Protein Data Bank. Geometries from each source were compared and pairs of refinements were performed to validate these new restraints. In addition to the restraints internal to the cluster, the CSD was mined to generate bond and angle restraints to be applied to the most common linking motif for Fe4S4: coordination of the four Fe atoms to the side-chain sulfurs of four cysteine residues. Furthermore, computational tools were developed to assist researchers when refining Fe4S4-containing proteins.
Highlights
Using accurate geometric restraints is essential in macromolecular crystallography in order to arrive at chemically meaningful atomic models
The experimental data, even when available at very high resolution, are typically unable to unambiguously define the exact conformation, and prior chemical knowledge is included in the form of geometric restraints
The bond distance from the Protein Data Bank (PDB) search is 2.30 Æ 0.03 A, which is in close agreement with the Cambridge Structural Database (CSD) results
Summary
Using accurate geometric restraints is essential in macromolecular crystallography in order to arrive at chemically meaningful atomic models. The experimental data, even when available at very high resolution, are typically unable to unambiguously define the exact conformation, and prior chemical knowledge is included in the form of geometric restraints. The use of high-quality experimental data, typically from small-molecule crystallography, to generate restraints and subsequent validation using a large number of refinements is a common paradigm. This procedure generally makes uses of the r.m.s. deviation between the target restraints and the refined models as a metric. We have used this approach to define accurate restraints for iron–sulfur clusters
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