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The origins of the Metatron's Cube design are lost in time. Clearly it is related to the Flower of Life, as they both explore the way circles, spheres and hyperspheres cluster together in the most energy efficient way.
In Metatron's Cube the center of each circle is connected to the center of every other circle.
Two hexagons are formed that create the projection of a Hypercube, and the projections of the 3D Platonic solids can also be found (although the dodecahedron requires the addition of an extra 6 small lines).
I believe the significance of Metatron's Cube is in its 4 dimensional form as the '24 cell' Vector Equilibrium that I call Metatron's Compass. You can find many different version of this in the Sacred Geometry Web Shapeways shop.
Metaron is the name of an Archangel said to be the scribe of God. He sits closest to the Throne and takes the Divine Utterances and records them in comprehensible form. Therefore the purpose of his 'cube' is clearly to define the symmetries of SpaceTime so that everything may be aligned with the blueprints of creation.
In this version we have separated the lines of Metatron's Cube into layers to make more visible its structure.