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Protocol publication

[…] The structure was solved by molecular replacement with PHASER () using residues 5–66 of E. coli Hfq as the search model. Electron density for RNA was apparent in the early maps. Maps were improved with density modification with PARROT using histogram matching with tRNA/aminoacyl-tRNA synthase experimental structure factors as the reference distribution. This structure has a similar solvent content and RNA/protein mass ratio as the RydC/Hfq crystals, and density modification with this method improved the map and visualisation of the RNA. The structure was refined using BUSTER () and with jelly body restraints in refinement with REFMAC (). The model was built using COOT (). The protein and RNA stereochemistry were validated by using both Coot validation tools and Procheck from the CCP4 suite (; ). The Ramachandran plot of the model places 92.9% of residues in most favoured regions, 5.4% in additional allowed regions, 1.6% in generously allowed regions, and none in disallowed regions. X-ray data collection and refinement statistics are summarized in . Figures were prepared using PYMOL (). The coordinates and structure factors have been deposited in the PDB with accession code 4v2s. […]

Pipeline specifications

Software tools Coot, PROCHECK, CCP4, PyMOL
Application Protein structure analysis
Organisms Escherichia coli