Hi, all I have encountered the high Rwork/Rfree values. Here is the story:
The glycosylated native protein structure is solved in the P212121 with unit cell parameters of 72.6, 78.0, and 112.5 and the all solution statistics are perfectly fine. I am trying to crystallize and solve the structure of its deglycosylated version. The deglycosylated protein crystallizes in the same morphology as glycosylated one. I expect both will share in the same space group with relatively similar unit cell parameters. Surprisingly the deglycosylated one has the unit cell parameter of 66.5, 70.5, and 137.0 (P21212 space group). These deglycosylated crystals diffract weakly but to 2.2A for the longer exposure time. At certain angles diffraction spots are streaky, although at the most of angles they are ok. I have processed the data in HKL2000, imosflm, and xds, which all suggested the P21212 space group (66.5, 70.5, and 137.0). The phaser suggests a solution at P22121, so the REINDEX is used to transform P21212 to P22121. However, after the first round of Refmac refinement, the Rwork/Rfree values are huge (0.35/0.41) and can’t be reduced further. The fitting of electron density map looks ok. I suspect the obtained crystals quality and resulting processed statistics is the reason for the observed high Rwork/Rfree values. Are there any suggestions? I have noticed that the unit cell volumes of both glycosylated (637065 Å3) and deglycosylated (642290 Å3) proteins are very similar. Is there a way I can transform one to the other? Thank you. Best, Haiying
