By keeping rest of the protocol same does centrifugation speed will have any effect on protein extraction from XL1-blue colonies
To sediment bacterial debris, 4000rpm should be fine, even just 10min. depends a little on vial size, of course.
Just compare different conditions in parallel by SDS-PAGE. Also eyeballing the supernatant for turbidity will give you valuable clues.
We always pelleted bacteria cells at 5000 xg for 10-15 min without issue for both DNA and protein purification. Lowering the speed for pelleting the cells shouldn't have an effect on your protein yield as long as it's sufficient to collect all of your cells.
Please be aware, however, that reporting centrifuge speed in RPM will be meaningless to anyone outside of your lab without the dimensions of your specific rotor. The actual centrifugal force (RCF), which is the important factor, will vary significantly with any fixed RPM depending on the radius of the rotor used.
It is advisable to use x g as the centrifıgation force which is a more universal unit instead of RPM as the reason is well defined above by Theresa Smith...
To find a common language and come to an agreement, the given question must be revised by giving the x g force you applied...
Thanks...İEA
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