2.4 Structure solution and refinement
For Ec ppnP, the diffraction data set was processed and scaled
using HKL3000 7. The phase was determined by
Selenomethionine-derived Ec ppnP using the program
hkl2map8. And all the native ppnP structures are
solved by Phaser with the structure of Se-Ec ppnP as the search
model 9. Cycles of refinement and model building were
carried out using REFMAC5 10, COOT11, and PHENIX 12 until the
crystallography reached a reasonable range. The details of data
collection and processing are presented in Table 1 . All
structure figures were prepared with PyMOL (DeLano Scientific). The
coordinates that support the findings of this study have been deposited
in the Protein Data Bank with accession codes for 7EYJ for NativeEc ppnP, 7EYK for Se-Ec ppnP, 7EYP for Pa ppnP, 7EYL
for St ppnP, and 7EYM for Vc ppnP, respectively.