Dear Chen, I am not an expert on SAD and MAD. However, at this stage I would not worry too much about density going through the 2-fold axis. There might be a sulfate ion or some other buffer component present at that position, or it may just be an artifact that will go away once the structure has been built and refined.
The questions I would worry about is: how much too small is your unit cell? Is it just crowded, say 25-30% solvent, or would your protein molecule not fit at all? Does the amount of solvent as estimated from your SAD/MAD maps agree with the amount of solvent obtained from the calculation of the Matthews volume? How many (SeMet?) sites do you expect, 6, more, less? If everything looks ok except that the unit cell is rather crowded, I would go ahead and try to build the structure. However, if even a single protein molecule would not fit in your unit cell, or you find many more sites than you can explain, you should start worrying about twinning. Even than the structure can probably be solved, but then you need some real experts! My 2 cents, Herman Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von Chen Zhao Gesendet: Montag, 31. März 2014 23:46 An: [email protected] Betreff: [ccp4bb] Space group problem? Dear all, I am now trying to phase a structure in C2 using anomalous scattering at 5-6 A. It is hard to improve the derivative resolution at the moment. Shelxd is able to locate 6 sites with a distinct CC and FOM. After density modification in shelxe, the contrast of the two enantiomers is 0.59/0.38 for SAD and 0.7/0.3 for MAD. When I looked at the electron density, the maps from SAD and MAD are similar, and the solvent boundary is quite clear. However, the problem is that the electron density blob passes through the 2-fold rotation axis, even at 3 rmsd contour level. Also, the unit cell seems to be too small for the molecule. I am afraid that the space group assignment is wrong, but I am a beginner so I nearly have no clue. I did reprocess the data in P1 and looked at the self-rotation function with a radius at 200 A. From the list it seems that there is only one 2-fold rotation axis. I am quite confused. Could anybody give me some hint of this problem? Thanks a lot in advance! Sincerely, Chen
