Stick to the low ground and fire charged beam shots directly at the SA-X to destroy it. Your beam must be fully charged to damage it. As it approaches, Space Jump over the SA-X to the other side of the floor while charging your beam, and release the shot when you land.

Only the Charge Beam and Screw Attack can damage the SA-X, though Ice Missiles can temporarily immobilize it. The Screw Attack is also ineffective, as Samus will take damage as well, even while the SA-X is frozen. The SA-X has a tendency to use its own Screw Attack as a counter-attack whenever Samus lands a blow.

Metroid Fusion is overtly a horror game, trapping Samus in a claustrophobic research station where all life (including other humans) has been eradicated and replaced by parasites capable of exaggerating their shapeshifting forms.