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Element mastery does affect crystal rank
It`s not mentioned on the page, but the mastery rank of the respective element does affect the crystal rank. r1 magic mastery, r7 fireball, r7 ice spear, r1 transmutation, r3 crystallization, r7 alch mastery.
Fire mastery is rank8, and can produce r9-rA fb crystals. Ice mastery is rank9, and can make rA-rB IS crystals. rA ice mastery resulted in rB-rC IS crystals.
Ice wand had only mana usage reduction upgrade, fire wand was phoenix with 40% speed -6% damage upgrade.
Edit: using a clean fire wand without damage reduction resulted in r9-r8 FB crystals with r7 FB and r8 fire mastery, ice spear was same as mentioned above.
Edit2: Tried again after ranking ice mastery to r5, and i`m getting r8-r9 IS crystals with very same equipment, titles, wand, weather, so it certainly does affect the mana crystal rank.