Actually, i know that you are trying to save money. The best solution would have been to get a compatible chassis from the compatibility list.
The reason being firstly it has been tested by Intel and it is condemned to work fine with them. And the system chassis fans will be regulated correctly as when configuring the SDR it will recognise the compatible chassis. So the system will be less loud than a reference chassis.
And other advantage is that you can contact Intel Customer Support for further advice if there is any problem.
Anyway since there is no tested reference chassis list on the Intel Website.
Firstly, i will check the power connectors specifications (cpu and power)
This can be found on the link below:
I will compare it with the power supply specifications that you are using and check if it meets all the requirements.
Now for the chassis:
Problems that can arise:
1) System fans may spin too loud even after configuring the SDR.
2) Front Panel may not work as it is not a compatible chassis.
3) USB Front header may not work.
The chassis is just the box. I have noted that the board S5000XVN supports the chassis Intel SC5299E.
And the other Intel board S5000VSA also supports the chassis Intel SC5299E.
And luckily for the board S5000VSA, there is a list of reference chassis.
So my point is that probably one of the chassis from the list for reference chassis for the board S5000VSA will work with your motherboard S5000XVN.
May be you can start by looking the specifications for the reference chassis and do your research.
Hope this may helps.