There are several posts here asking how to power a board from just the User USB port. I am using the STM32F407G-DISC1 rev E boards. Here is my solution.
A Schottky diode (1N5817 or equivalent) is soldered with its anode connected to the VBUS pin on the User USB micro connector, and its cathode connected to 5V. This has a similar effect as the existing Schottky diode D1 that connects the USB debug port's VCC (U5V) to 5V.
The easiest way to attach the diode on this board is from C49 (VBUS) to P2 pin 3 (5V). See the attached picture.
This works well and won't affect operation even if the User USB is used as a host, but my application uses this USB as a device. I can now run the board standalone, or even have it keep running while debugging and then disconnect the debug USB cable.