The combination of laser cooling and the fountain design allows NIST-F1 to observe cesium atoms for longer periods, and thus acheive its unprecedented accuracy. Traditional cesium clocks measure room-temperature atoms moving at several hundred meters per second. Since the atoms are moving so fast, the observation time is limited to a few milliseconds. NIST-F1 uses a different approach. Laser cooling drops the temperature of the atoms to a few millionths of a degree above absolute zero, and reduces their thermal velocity to a few centimeters per second. The laser cooled atoms are launched vertically and pass twice through a microwave cavity, once on the way up and once on the way down. The result is an observation time of about one second, which is limited only by the force of gravity pulling the atoms to the ground.
As you might guess, the longer observation times make it easier to tune the microwave frequency. The improved tuning of the microwave frequency leads to a better realization and control of the resonance frequency of cesium. And of course, the improved frequency control leads to what is one of the world's most accurate clocks.