Computational protocol: Regulation of Response Regulator Autophosphorylation through Interdomain Contacts*♦

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[…] Positions of five of the eight selenium sites were determined from the peak wavelength utilizing the single-wavelength anomalous dispersion phasing protocol implemented in CNS with a mean figure of merit of 0.283 and phasing power of 1.24 (). Initial phase estimates extending to 1.9 Å were improved with solvent flipping and density modification. A starting model was generated utilizing the model building tools in COOT (). Density corresponding to the BeF3− moiety was clearly visible after several rounds of refinement that included simulated annealing, maximum likelihood, and temperature factor refinements in CNS (), followed by model building with COOT. Water molecules were added to positive difference Fourier peaks >2.5σ. The model was refined to 1.9 Å with an R factor of 0.189 and an Rfree value of 0.231. It contains 234 residues, 125 water molecules, and two magnesium, two beryllium, and six fluoride atoms. All residues lie in the allowed region of the Ramachandran plot and exhibit favorable stereochemistry as defined by PROCHECK (). [...] The structure of MtrAN was solved by molecular replacement using PHENIX () and the N-terminal domain of full-length MtrA (Protein Data Bank code 2GWR) as a search model. The structure was rebuilt in place and iteratively refined using PHENIX and COOT. The model contains four protein molecules (amino acid residues 5–120 (A), 6–120 (B), 5–121 (C and D)), 155 water molecules, and four Mg2+ ions. All residues lie in the favored region of the Ramachandran plot and exhibit favorable stereochemistry as defined by MolProbity ().Data collection and refinement statistics for DrrBN, DrrDN, and MtrAN are given in supplemental Table S2. Figures were generated using the PyMOL Molecular Graphics System (Schrödinger LLC). […]

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