Hi, Phil, Sorry for the confusion. I did use MR solution/data combination to run Refmac and I did reindex the data and re-run MR with the reindexed MTZ file and run refmac. Both gave the above given high Rwork/Rfree values (0.35/0.41). If I refine the original MTZ native data file with the PDB file Phaser wrote, the R values are extremely high (0.50/0.52). Thank you for these points you made.
1. throw the thing at Arp/wArp and look hard at the maps you get out. The structure might have changed more than you thought. “Arp/wArp generated structure has too many dummy atoms with GLY chains and it’s hard to interpret the map”. 2. rescale the data in P1 and put it into Pointless and/or Xtriage to check for twinning and point group assignment “It gave P22121 as Phaser solution pointed. No twinning is suspected.” 3. I'm fairly sure that the (72.6, 78.0, 112.5) and (66.5, 70.5, 137.0) cells are unrelated but #2 will show that. 4. If all else fails solve it in P1 and find the space group "by inspection" afterwards I put the rescaled P1 data and ensemble model (P212121 glycosylated solution) to Phaser, I haven’t seen any distinctive solution. I start to suspect the P22121 solution is wrong. I have three domains in the structure, maybe the domain is swapped? Maybe I should start to grow better quality crystals in order to solve it. Thank you. Haiying On Mon, Jun 24, 2013 at 9:23 AM, Phil Jeffrey <pjeff...@princeton.edu>wrote: > Haiying, > > As far as I can tell you've got a successful solution in molecular > replacement via Phaser and then gone and refined it in the wrong space > group. > > Based on what you've told us: you took your initial data in primitive > orthorhombic and solved for the structure in Phaser while sampling all > possible space groups. Phaser is telling you that your *original* data > indexing is truly space group P22(1)2(1) and if you take that m.r. > solution/data combination and simple *assign* the space group it should > work in Refmac. In fact Phaser should have written the correct space group > in the PDB file header. > > If you refine your original MTZ native data file with the PDB file Phaser > wrote, what do you get ? > > You seem to have reindexed the data but not rotated the model (or re-run > molecular replacement). That makes the model and data out-of-sync. Phaser > does not reindex the data internally, and that's why it tries eight space > groups in primitive orthorhombic rather than just the minimal set P222, > P222(1), P2(1)2(1)2, P2(1)2(1)2(1). The others that it tries are > alternative settings of these space groups (where appropriate). > > If you want to refine in P2(1)2(1)2 then reindex the data (h,k,l) -> > (k,l,h) and re-run molecular replacement with the reindexed MTZ file. > > > If the above is a misinterpretation of what you wrote, my alternative > advice on this is: > > 1. throw the thing at Arp/wArp and look hard at the maps you get out. The > structure might have changed more than you thought. > 2. rescale the data in P1 and put it into Pointless and/or Xtriage to > check for twinning and point group assignment > 3. I'm fairly sure that the (72.6, 78.0, 112.5) and (66.5, 70.5, 137.0) > cells are unrelated but #2 will show that. > 4. If all else fails solve it in P1 and find the space group "by > inspection" afterwards > > Phil Jeffrey > Princeton > > > > -- Haiying Bie, Ph.D. Postdoc Fellow at Michael James lab 4-29 Medical Science Building Department of Biochemistry University of Alberta, Edmonton, T6G 2H7
