Dear Herman, Thank you so much for your suggestions. The density that passes through the rotational axis is so strong and extended that can be considered as a significant portion of the molecule. However, some density in the middle might show some features. I have no experience and this could be only artifact.
The unit cell seems to be able to fit 1-2 molecules. But if there is one molecule/ASU, the solvent content is about 89%, which is possible but unlikely. Although the resolution of the crystal is not high, it is rather rigid and easy to handle, which might indicate a not-too-high solvent content. I soaked the native crystal with heavy atom compounds and I have no clear idea of the relationship between metal binding and sequence, so I don't know how many sites to expect. Best, Chen On Tue, Apr 1, 2014 at 9:42 AM, <[email protected]> wrote: > 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 >
