Let's say we have a PWM fan Thermalright TY-140. It has a speed range of 900-1350 RPM. Let's assume we use a motherboard which can send duty cycles in range 50%-100% to PWM fan header. What is the minimum RPM I can achieve with this combination?

1150 RPM?

The mobo in question is MSI Z77A-GD65. It has great specs otherwise but the fan controls seems to suck big time.

PWM fans have a fan profile. Maximum (100%) duty cycle should always equal maximum rpm, but the minimum duty cycle setting is another matter. With some fans 0% duty cycle = 0 rpm, but with many the minimum rpm is set at around 30% or 40% duty cycle, and what rpm that translates into depends on the fan. In the case of the Thermalright TY-140 the minimum duty cycle is 30%, and the fan should run at around half speed at this setting. Despite the spec quoted by Thermalright the true speed range of this fan is more like 650 rpm to 1300 rpm. So 30% duty cycle on this fan = around 650 rpm. Any setting less than 30% will result in the same speed.

I am familiar with the MSI Z77A-GD65, having tried one that was on demo. All I could find under the fan control section in the BIOS was a maximum duty cycle setting which did not seem to go below 50%, so not particularly helpful. Part of the reason is that MSI seem to have positioned the GD65 as an overclockers board. Certainly it is a very capable board if this is what you want. But as a consequence there seems to be an emphasis on features relevant to overclockers such as the quality of the motherboard power supply components and the provision of no more than basic fan controls.

As to a solution, it might be worth trying the Scythe Slip Stream 120mm PWM Adjustable Fan SY1225SL12HPVC. This fan has a manual control which enables you to set the PWM range, so you might be able to set a lower RPM with this than you can get with the Thermalright. This is a potential source http://www.jimms.fi/tuote/SY1225SL12HPVC.

While PWM fans have a range its not always what the manufacturer advertises, or it can vary. In my expirience,

Intel DH61DL can drop the TY140 to 700rpm (check mini mi sig for proof) and can also drop the Cythe Kama Flex PWM around 250rpm (specs implies 300-1600)
Intel DQ67 can drop the Scythe Kama Flex PWM to 200 (check HTPCMI build on sig), same mobo same behavior with the Scythe Slipstream PWM (300-1600) that came with the mugen 3.

Hi, I don't think motherboards have a minimum PWM % they can send the fan, more like a minimum programmed in to the BIOS/UEFI.
My experience is over-ridding with Speedfan (or the like) allows you to send what ever PWM % you like to the fan.

How it reacts to that is another matter.
You might take a look at the official spec document, pages 12 -16 are the interesting ones.

All the PWM fans I've used have bottomed at at 25-30%, sending a lower PWM has made no difference to minimum speed. I have TY-140s on my CPU cooler and also find the minimum speed to be ~690rpm @ 30% PWM. According to the official doc it should be 30% of max speed, ie 30% of 1300rpm = 390rpm (+10% allowance = 40% = 520rpm) which I would much prefer to 690rpm minimum.

However... I've wired a Zalman fanmate in to the +ve and -ve wires of the fans so I can adjust the power supply voltage the fan sees, the speed and PWM wires are still directly connected to the mobo header. What this allows is to adjust the operating range of the fan, with bit fiddling getting the right level I now have a 500 to 1000rpm fan. (still on PWM speed control and reporting its speed)

Some Scythe PWM fans come with a back plate fan controller that has two modes. (IIUC) In one mode it directly controls the fans speed like a normal 3pin fan and controller. In the other mode it acts like my fanmate, the fan's speed still varies with PWM signal but the range it opperates over is adjusted. E.g. you can set fan to be 500 ~ 1600rpm range or 300 ~ 1200rpm or whatever you like in between. Scythe fan with controller

Hope this helps, Seb