[sharp-discuss] Refining Se-met sites

[gte977x@mail.gatech.edu]

Dear SHARPusers:

I am trying to phase a protein structure using Se MAD data set in P212121. I
found 30 Se sites in SOLVE out of total of 52 with z score = 102.56 and fom =
0.39. The 30 sites were found using SAD data to 3A in SOLVE. I input the SOLVE
output into SHARP and tried refining against the whole MAD data. The refined
maps didn't show Se in density for either of the hands.

Next, I tried refining sites using SAD data to 2.4 A resolution in SHARP. The Se
were in density and there were lots of positive peaks in residual maps. I went
ahead and did solvent optimization. SHARP gave optimal solvent content of 38%
which is not believeable. I expect the solvent content to be around 63% so I
checked these maps for the secondary sturctures. Map have connectivity but no
obvoius sec. str. 

In third set of trials, I tried to use just the remote and peak. Phasing stats
looked much better than SAD but residual maps had lot of negative peaks and 5 to
6 peaks overlapping with HA positions. EDEN maps did have Se in density. 

In fourth run,using 2 wav. data (remote and peak) I marked all the f' and f" for
refinement. In this case there are lot of positive peaks in residual maps but Se
are not in density again.

I am pretty confused by these results. Any suggestions will be greatly appreciated.


Extra info:
Although I had systematic absences for all three axes I ran solve in P222,
P21212 and P2221 also. P212121 sats were best.
 
While integrating my data, Cells over the 3 wav.are:

Pk = 90.3900  163.7399  173.4095   90.0000   90.0000   90.0000
remote =  90.4162  163.2355  173.5318  90.0000   90.0000   90.0000
inf = 90.5415  163.8508  173.8143   90.0000   90.0000   90.0000

I reindexed these data sets separately in P212121 and then scaled them using
scaleit.

Akanksha