We deal with usage of plane-wave density functional calculations of crystallites formed of 100-200 transition metal atoms to mimic larger experimentally treated particles. A series of model Pd clusters containing up to 225 atoms is chosen as an example. We focused on the description of size-dependent geometric parameters and binding energies of these clusters as compared with previous benchmark calculations; evolution of the particle electronic structure with increasing size has also been addressed. The high performance of the plane-wave calculations for transition-metal nanoparticles has been documented. Implications of this work on broadening opportunities to design and study realistic models of catalytic systems are outlined.