Solubility of the deglycosylated protein is often a problem. Some solutions:
1. Increase the buffer concentration or salt concentration. None of the
Endo F enzymes including PNGase F are affected by even 0.7 M NaCl
2. Decrease the protein concentration.
3. Increase the temperature. Why are you incubating at 4 C ?
4. Change the pH (but don't go over pH 6 with Endo F2.
You may be able to redissolve the precipitated protein.
Where are you getting Endo F2 from these days?
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