Mn3Pd20P6 crystallizes in the cubic Fm-3m space group. There are two inequivalent Mn sites. In the first Mn site, Mn(1) is bonded to four equivalent Pd(1) and twelve equivalent Pd(2) atoms to form distorted MnPd16 tetrahedra that share edges with six equivalent Mn(1)Pd16 tetrahedra, edges with twelve equivalent Pd(1)MnP3Pd6 tetrahedra, faces with four equivalent Mn(2)Pd12 cuboctahedra, and faces with four equivalent Pd(1)MnP3Pd6 tetrahedra. In the second Mn site, Mn(2) is bonded to twelve equivalent Pd(2) atoms to form MnPd12 cuboctahedra that share edges with twenty-four equivalent Pd(1)MnP3Pd6 tetrahedra and faces with eight equivalent Mn(1)Pd16 tetrahedra. There are two inequivalent Pd sites. In the first Pd site, Pd(1) is bonded to one Mn(1), six equivalent Pd(2), and three equivalent P(1) atoms to form distorted PdMnP3Pd6 tetrahedra that share corners with three equivalent Pd(1)MnP3Pd6 tetrahedra, edges with three equivalent Mn(2)Pd12 cuboctahedra, edges with three equivalent Mn(1)Pd16 tetrahedra, edges with three equivalent Pd(1)MnP3Pd6 tetrahedra,  a faceface with one Mn(1)Pd16 tetrahedra, and faces with six equivalent Pd(1)MnP3Pd6 tetrahedra. In the second Pd site, Pd(2) is bonded in a 14-coordinate geometry to one Mn(2), two equivalent Mn(1), four equivalent Pd(1), five equivalent Pd(2), and two equivalent P(1) atoms. P(1) is bonded in a 8-coordinate geometry to four equivalent Pd(1) and four equivalent Pd(2) atoms.
Mn3Pd20P6 crystallizes in the cubic Fm-3m space group. There are two inequivalent Mn sites. In the first Mn site, Mn(1) is bonded to four equivalent Pd(1) and twelve equivalent Pd(2) atoms to form distorted MnPd16 tetrahedra that share edges with six equivalent Mn(1)Pd16 tetrahedra, edges with twelve equivalent Pd(1)MnP3Pd6 tetrahedra, faces with four equivalent Mn(2)Pd12 cuboctahedra, and faces with four equivalent Pd(1)MnP3Pd6 tetrahedra. All Mn(1)-Pd(1) bond lengths are 2.75 Å. All Mn(1)-Pd(2) bond lengths are 3.31 Å. In the second Mn site, Mn(2) is bonded to twelve equivalent Pd(2) atoms to form MnPd12 cuboctahedra that share edges with twenty-four equivalent Pd(1)MnP3Pd6 tetrahedra and faces with eight equivalent Mn(1)Pd16 tetrahedra. All Mn(2)-Pd(2) bond lengths are 2.93 Å. There are two inequivalent Pd sites. In the first Pd site, Pd(1) is bonded to one Mn(1), six equivalent Pd(2), and three equivalent P(1) atoms to form distorted PdMnP3Pd6 tetrahedra that share corners with three equivalent Pd(1)MnP3Pd6 tetrahedra, edges with three equivalent Mn(2)Pd12 cuboctahedra, edges with three equivalent Mn(1)Pd16 tetrahedra, edges with three equivalent Pd(1)MnP3Pd6 tetrahedra,  a faceface with one Mn(1)Pd16 tetrahedra, and faces with six equivalent Pd(1)MnP3Pd6 tetrahedra. All Pd(1)-Pd(2) bond lengths are 2.99 Å. All Pd(1)-P(1) bond lengths are 2.47 Å. In the second Pd site, Pd(2) is bonded in a 14-coordinate geometry to one Mn(2), two equivalent Mn(1), four equivalent Pd(1), five equivalent Pd(2), and two equivalent P(1) atoms. There is one shorter (2.70 Å) and four longer (2.93 Å) Pd(2)-Pd(2) bond lengths. Both Pd(2)-P(1) bond lengths are 2.36 Å. P(1) is bonded in a 8-coordinate geometry to four equivalent Pd(1) and four equivalent Pd(2) atoms.