JISCMail - CCP4BB Archives

First you say that both crystals are processed as P21, which you would expect a very strong peak (100% of your origin peak) on kappa/chi=180 at the b* axis (one of the major axes of your map); this arises from the crystallographic symmetry. Where this axis is depends on what the conventions are of the program you are using. Your SRF has a major peak along Z, but is that the b* axis? (My b* axis is always placed North-South or your X, á la the Rossmann conventions. I don’t know the conventions for Molrep) Then you see major off-axial peaks. The sad thing about your off-axial peaks is that they are badly split.

The second problem is that the second crystal shows very strong peak (1001% of your origin peak) on kappa/chi=180, but at different position (along Y). The control peak is the expected peak which arises from the P21 crystallographic symmetry. If the data sets were processed as P21, they should be indexed with the 2-fold axis along b/b*, thus the control peak is the expected peak which arises from the P21 crystallographic symmetry. Once that peak appears in the same place on each map, you can then compare the maps with more confidence.

The third problem is that all your maps have the “appearance" of mirror symmetry across the x-axis, which would be expected as it is the consequence of the P2(1) symmetry and you are looking at a hemisphere. But it suggests that the 2-fold axis is along Y (b/b*). Then map 1 is missing the expected peak on kappa/chi=180 at the b* axis.

Final comment is that the maps labeling suggest that the radius of integration is 62-66 Å, which is way, way too large, even for an empty unit cell. If it is, reduce it down to 20-30 Å to avoid intermolecular cross-peaks and see if the maps become clearer. I have attached a SRF map from a P21 crystal form (radius of integration = 20 Å, resol. = 2.8 Å) with the 2-fold axis indexed along b/b* (Y) from polarrfn; note the “appearance" of mirror symmetry perpendicular to across the b/b*-axis (North-South or y-axis).