Help with build

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I think you'd be much happier with this. You can change the case but your compatibility issues were from choosing a case with no front USB 3.0 ports. As long as the width of the case has enough room for a tower cooler in case you choose to use one later, has two top and two front, or one front 200mm, fans or fan locations, and a bottom mounted power supply location, it will work fine.

PCPartPicker part list / Price breakdown by merchant

CPU: Intel Core i5-4460 3.2GHz Quad-Core Processor ($187.89 @ OutletPC)
Motherboard: ASRock Z97 PRO3 ATX LGA1150 Motherboard ($89.99 @ Newegg)
Memory: Kingston Fury Red Series 8GB (2 x 4GB) DDR3-1866 Memory ($81.99 @ NCIX US)
Storage:...
I think you'd be much happier with this. You can change the case but your compatibility issues were from choosing a case with no front USB 3.0 ports. As long as the width of the case has enough room for a tower cooler in case you choose to use one later, has two top and two front, or one front 200mm, fans or fan locations, and a bottom mounted power supply location, it will work fine.

PCPartPicker part list / Price breakdown by merchant

CPU: Intel Core i5-4460 3.2GHz Quad-Core Processor ($187.89 @ OutletPC)
Motherboard: ASRock Z97 PRO3 ATX LGA1150 Motherboard ($89.99 @ Newegg)
Memory: Kingston Fury Red Series 8GB (2 x 4GB) DDR3-1866 Memory ($81.99 @ NCIX US)
Storage: Seagate Barracuda 1TB 3.5" 7200RPM Internal Hard Drive ($53.98 @ OutletPC)
Video Card: Sapphire Radeon R9 280 3GB Dual-X Video Card ($184.99 @ Newegg)
Case: Thermaltake Commander MS-I ID ATX Mid Tower Case ($34.99 @ Micro Center)
Power Supply: XFX 650W 80+ Bronze Certified ATX Power Supply ($49.99 @ NCIX US)
Total: $683.82
Prices include shipping, taxes, and discounts when available
Generated by PCPartPicker 2014-10-05 00:27 EDT-0400

I also upgraded you to a Z97 motherboard, and faster RAM. The Sapphire card is also a better choice than the HSI.
 
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