Crystallographic coordinates The coordinates of each atom are expressed as fractions of each side of the unit cell. These sides are usually not of the same length and frequently not at right angles to each other.
Most programs convert crystallographic coordinates to cartesian coordinates.
An average small molecule which is about 12-15 angstroms long will have x, y, z coordinates between about 0 and 15 if one of the atoms at one end of the molecule lies at the origin 0,0,0. In very large molecules such as proteins the coordinates can be quite large numbers. This is not always present as some programs assume you only work in cartesian cordinates. Here one atom is taken as the origin all atoms defined with respect to this atom. The second atom is defined as being a certain distance from the first.