Dear Niu, I had an interesting pseudo-translation case recently where my off-origin peak was located near the centre of the unit cell (fractions a=0.5, b=0.46, c=0.5) of a P222 symmetry. Processing and phasing in P222 looked reasonable and the model could be built. I had background density which I thought of as water. I got suspicious when I identified density for a helix which was near my build main chain but could not be joined and built or be accounted for by looking at symmetry mates. Moreover I got stuck in refinement with R/Rfree 25/30%. I could identify which part of the protein caused me the trouble on crystal packing and the appearance of the off-origin peak. In my case it was the C terminus. So I used a new construct with swapped purification tag (N to C terminus). This altered the peptide sequence for the C terminus and allowed the protein to pack nicely into I222. This turned my off-origin peak into a true symmetry operator.
I also had reasonable processing and phasing results for P2 and C2. So besides the strength of your off-origin peak it may be off some use to look at the location. HTH Melanie ________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Niu Tou [niutou2...@gmail.com] Sent: 14 November 2013 23:58 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Weird MR result Dear Phil, I used PHASER to do the task. I have double checked and both files have the same prefix, so they are from the same output. I have also checked the headers again, they have the same spacegroup. Actually I was trying to search for two different molecules but only one was found. The spacegeoup is P2 and I am quite sure it is not P21 from system absence. One possibility is that the space group was wrong, since there is a 95% off origin peak. There are several choices from data processing, P1, P2, C2 C222, all have this large off origin peak. I wonder if this 95% peak can tell some information? It will not surprise me if this result is incorrect, however how could these regular density be? Best, Niu On Thu, Nov 14, 2013 at 5:47 PM, Phil Jeffrey <pjeff...@princeton.edu<mailto:pjeff...@princeton.edu>> wrote: Hello Niu, 1. We need extra information. What program did you use ? What's the similarity (e.g. % identity) of your model. What's your space group ? Did you try ALL the space groups in your point group in ALL the permutations (e.g. in primitive orthorhombic there are 8 possibilities). 1a. My best guess on limited info is that you've got a partial solution in the wrong space group with only part of the molecules at their correct position. 2. I recently had a very unusual case where I could solve a structure in EITHER P41212 or P43212 with similar statistics, but that I would see interpenetrating electron density for a second, partial occupancy molecule no matter which of these space groups I tried (and it showed this when I expanded the data to P1). Might conceivably be a 2:1 enantiomorphic twin, in retrospect, but we obtained a more friendly crystal form. I hope you don't have something like that, but it's possible. Phil Jeffrey Princeton On 11/14/13 5:22 PM, Niu Tou wrote: Dear All, I have a strange MR case which do not know how to interpret, I wonder if any one had similar experiences. The output model does not fit into the map at all, as shown in picture 1, however the map still looks good in part regions. From picture 2 we can see even clear alpha helix. I guess this could not be due to some random density, and I have tried to do MR with a irrelevant model without producing such kind of regular secondary structure. This data has a long c axis, and in most parts the density are still not interpretable. I do not know if this is a good starting point. Could any one give some suggestions? Many thanks! Best, Niu
