I think you are right about the absences—not just fortuitous, suggesting something “screwy” in the spacegroup. Why don’t you try autobuilding in Buccaneer in both P31 and P32? If you have any weak anomalous scatterers, like S, you can use partial model phases in Phaser to do MR-SAD and then autobuild.

And give ArpWarp a try as well.

JPK

From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Chen Zhao
Sent: Tuesday, July 19, 2016 3:23 PM
To: [log in to unmask]
Subject: [ccp4bb] Doubts about space group determination

Dear crystallographers,

I am now working on a 3.6 A dataset and I have some doubts on space group determination. Most importantly, I would like to learn and understand more about this procedure.

The data quality is not ideal and there is some radiation damage. Base on CORRECT in XDS, it looks like P3_12, P3_1, C2 and P1 are all compatible with the reflection intensities. I attached the screenshot of the table here.

MR is able to find a single solution (partial model occupies 63% of the whole) with high score in all space groups listed above. However, after a refmac run, only space group P1 gives a R-free below 40%, and all other space groups yields R-free factors about 50%. (I think I used the Rfree generated based on point group symmetry but I might not have done it in the right way.) Besides, the desired electron density (although only a very small region is clear) is the best in P1, present in P3_1, barely present in P3_12 and almost completely absent in C2. Therefore, it looks like the space group should be P1.

However, the pseudo-procession images (attached) show clear systematic absences for 3_1 axis. Although to my untrained eyes, I cannot tell with 100% confidence about the 3-fold symmetry in the reflection intensities on the hk0 plane, even though the lattice pattern looks like 3-fold.

Twinning test does not suggest significant twinning.

I just don't have much experience, but assuming it is P1, is it possible for NCS to have such perfect absences? Any suggestions and comments would be much appreciated!

Sincerely,

Chen