2.4. Structure solution and refinement  

The structure was solved by the molecular-replacement method using Phaser (McCoy et al., 2007 ▸) with the coordinates of E. coli PNP at 0.99 Å resolution (PDB entry 4rg2) as a search model. Structure refinement was carried out using REFMAC5 (Murshudov et al., 2011 ▸). Manual rebuilding of the model was performed using the Coot interactive graphics program (Emsley et al., 2010 ▸), and electron-density maps were calculated with 2|F _o| − |F _c| and |F _o| − |F _c| coefficients. In the electron-density map calculated with |F _o| − |F _c| coefficients at the 2.0σ level, clear electron density was observed in the active site of each subunit and could be interpreted as an acyclovir molecule. Clear electron densities for sulfate ions, which are present at high concentration in crystallization solution, were also found (Fig. 2 ▸ a). A number of water molecules were located in the difference electron-density maps. The atomic coordinates of the PNP–ACV complex have been deposited in the Protein Data Bank as entry 5i3c. Refinement statistics are summarized in Table 4 ▸.

(a, b) Acyclovir in the active site of the E. coli PNP subunit. The electron-density map was calculated without ligands with coefficients 2|F _o| − |F _c| and is contoured at 2σ for the two conformations of acyclovir. (c) A hexameric molecule of E. coli PNP with an acyclovir molecule and a sulfate ion in the active sites. These figures were created using PyMOL (https://pymol.org/2/).

Values in parentheses are for the outer shell.