Mana Crystals are used to purchase Booster packs (to gain additional cards), health packs, creation of a Coalition, and Planeswalkers. The original 5 Planeswalkers (not including Nissa which is Free) are available at a discounted price of 50 Crystals each so they are attainable for all new players. Players can also rename their Coalition for a small mana crystal purchase.
Mana Runes are used to level up your Planeswalkers.
Mana Jewels are used to purchase the Elite Pack, which offers a single card. This pack guarantees a Mythic, and has a chance of a Masterpiece card. Every 2 weeks, a new selection of Mythic and Masterpiece cards will be available through the Elite Pack in the Vault. You can check out the current rotation of cards by clicking the "View Cards" info button.