Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from…

By A. Brunger, D. Das, Ashley Deacon, Joanna C. Grant, T. C. Terwilliger, Randy J. Read, Paul D. Adams, Michael Levitt, Gunnar F. Schröder. 2012

30 citations recorded by the source corpus.

DEN refinement and automated model building with AutoBuild were used to determine the structure of a putative succinyl-diaminopimelate desuccinylase from C. glutamicum. This difficult case of molecular-replacement phasing shows that the synergism between DEN refinement and AutoBuild outperforms standard refinement protocols.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, background): “The protocol is particularly useful for low-resolution diffraction data (Brunger et al., 2012).”
Revisit of reconstituted 30-nm nucleosome arrays reveals an ensemble of dynamic structures (2018, methodology): “We then manually located the globular domain (PDB code: 1HST chain B) to fit the difference map, and further refined using the DEN-based strategy for low resolution [68].”
Model morphing and sequence assignment after molecular replacement (2013, methodology): “To develop and assess the effectiveness of our procedure for sequence assignment, we chose a challenging molecularreplacement structure solution that we recently completed using a combination of DEN refinement, automated and manual procedures (Brunger et al., 2012).”