The crystal is worth an estimated USD 1.5 million, and was found in Venezuela.
Researchers at Los Alamos National Laboratory used a neutron scanner to effectively look inside the 217.78 gramme piece of gold, roughly the size of a golf ball.
Neutrons, different from other probes such as X-rays and electrons, are able to penetrate many centimetres deep into most materials, researchers said.
"The structure or atomic arrangement of gold crystals of this size has never been studied before, and we have a unique opportunity to do so," Geologist John Rakovan from Miami University said.
Revealing the inner structure of a crystal without destroying the sample allowed Rakovan and collaborators to prove that this exquisite nugget, which seemed almost too perfect and too big to be real, was a single crystal.
Its owner provided the samples to Rakovan to assess the crystallinity of four specimens, all of which had been found decades ago in Venezuela.
Three of the four samples turned out to be single-crystal pieces of gold, rather than the commonplace multiple-crystal type.
Of particular interest was a golf-ball-shaped nugget that at one time was believed to be the world's largest trapezohedral gold crystal.
In 2006 the crystal had been rejected at auction over questions of authenticity, researchers said.
Further interpretation of the results will also provide an understanding of how the rare pieces may have formed before they were slightly deformed while being washed down in ancient stream sediments.
"The gold single crystals are so far the largest single crystals characterised on HIPPO," said Sven Vogel, instrument scientist for the high-pressure/preferred orientation (HIPPO) instrument.