In the absence of knowing the use and programs for which this system is intended (MATLAB?), I can only generalize, but I would agree with Outlander_04 that the proposed LGA1366 is backwards-looking technology. It's possible to improve capabilities significantly for a relatively small additional cost.
It would also be easier to make suggestions when a budget is specified. There are also no storage drives listed.
The positive of the idea is that the Xeon E5645 is about $600- inexpensive for a 6-core Xeon, and would provide adequate PCIe lanes, but it is also a couple of generations past, using 1333 RAM -today, V2 Xeons can use 1600- and some 1866, the max memory bandwidth of the E5645 is 30GB/s- modern Xeons are 56GB/s- and the clock speed of 2.4 / 2.67GHz is acceptable for a server, but simulation benefits greatly from clock speed. In Passmark benchmarks>
(2) Noctua NH-D14 120mm & 140mm SSO CPU Cooler > $160 ($80 ea.) (High performance CPU cooling for extended - that is running continuously, full core simulation slogs is essential) (These are quite large > Verify compatibility with rackmount chassis.) (See alternate enclosure suggestion)
Motherboard > ASUS Z9PE-D8 WS Dual LGA 2011 Intel C602 SATA 6Gb/s USB 3.0 SSI EEB > $534
RAM > 128GB (8) Samsung or Kingston 1X16GB 240-Pin DDR3 SDRAM ECC Registered DDR3 1600 Server Memory > about $1400 >(note 1600 speed instead of 1333) (VERIFY model compatibility with ASUS aproved vendors list)
HD: SAMSUNG 840 Pro Series MZ-7PD256BW 2.5" 256GB SATA III MLC Internal Solid State Drive (SSD)
Video Card: NVIDIA Quadro K600 VCQK600-PB 1GB GDDR3 PCI Express 2.0 x16 Low Profile Workstation Video Card (I'm assuming by this choice that there is almost no 3D component in your work, that is it's MATLAB, statistical, and results are expressed in waveforms and graphs. If you are doing any 3D dynamic modeling of gas, particle, thermal, atmospheric / oceanic, dynamic structural simulation / analysis (e.g. flight dynamics, airframe)> then I would recommend a Quadro K5000, about $1,800.)
Case > CaseLabs Merlin ST10 Case with options, about $475 (As an alternative approach > You probably have good reasons to have this system in a rackmount, but this an alternative that make assembly /configuration / testing easier and provides very good airflow and extremely good cooling apparatus potential. This case provides 14X 5.25" drive bays. CaseLabs has an extremrly wide selection of options and the system may be assembled and configured as a kind or completely open test platform.
(2) CORSAIR Hydro Series H110 Extreme Performance Water/Liquid CPU Cooler. 280mm > $220 ($110 ea.) (High performance CPU cooling for extended - that is running continuously, full core simulation slogs is essential)
Power Supply > SeaSonic X Series X-850 (SS-850KM3 Active PFC F3) 850W ATX12V v2.3 / EPS 12V v2.91 SLI Ready CrossFire Ready 80 PLUS GOLD Certified Full Modular Active PFC Power Supply > $270
NZXT Sentry-2 5.25" Touch Screen Fan Controller > $28.
I believe a lot of benefit - (almost +50% computational power) would be achieved with an additional expenditure of only about +$150 for CPU's and using the more forward-looking LGA2011 platform. Importantly, this system could be uprated to use 8, 10, 12, and possibly 15-core Xeons. For example >