Ensemble refinement
Crystallographic coordinates and diffraction data for theArchaeoglobis fulgidus complex (PDB3MM5) were downloaded and
subjected to several types of refinement approached using the current
Python-based Hierarchical Environment for Integrated Crystallography
(Phenix) software (42–44). First, the number of TLS groups was
increased using the automatic definition available in Phenix, and some
manual refinement was performed by alternating Coot manual rebuilding
and Phenix minimization. Then, the refined structure was submitted to
ensemble refinement using Phenix_ensemble with parameters adjusted
according to the default recommendations (pTLS = 1; wxray = 0.5 and Tx
=0.6 ).