Hi Sabine, my first guess would be that you are overlooking half of the reflections meaning the cell has really twice the volume. Is the list of difference vectors in IDXREF.LP clean in this respect?
Best, Kay On Wed, 16 Nov 2016 17:26:59 +0100, Sabine Schneider <sabine.schnei...@cup.uni-muenchen.de> wrote: >Hello everybody, > >I got a problem with solving and refining a structure of a small protein >of 20kDa, where we just swapped two residue at the surface by mutation >(AF vs FA). > >For the FA variant we got three crystal forms, where we had no problem >whatsoever with MR and refinement >- P6522 cell 63 63 184 ~2.9A >- P21212 cell: 53 62 109 ~3A >- P212121 cell 40 43 96 ~1.8A > >However with the AF-variant we only got one crystal (out of 50) that >diffracted reasonable well to ~2.4A at the synchrotron. And now the >problem starts: initially the data appear to be orthorhombic, but: > >- SG18/19: cell 59 91 109 (I noticed that the b-axis is longer by 1/2b >compared to the other variant?!) >-> running phaser checking all possible alternative SGs found initally 2 >mols/AUS in SG18, but since there was still space (and density!) I let >it search for another one (increased the clash tolerance) >SOLU SET RFZ=7.7 TFZ=11.8 PAK=0 LLG=141 TFZ==13.9 RFZ=3.0 TFZ=11.2 PAK=0 >LLG=280 TFZ==17.1 LLG=288 TFZ==17.3 RFZ=5.9 TFZ=16.0 PAK=16 LLG=979 >TFZ==15.3 LLG=1479 TFZ==17.4 > >- However the third molecule than clashes partly > >- running refmac: R/Rfree stays in the high 40 > >- analysing the data with Xtriage indicates tNCS > >- I also tried P212121, P21 and P1, always with the same result: space >as well as density between the proteins; placing more protein molecules >results in clashes (i.e. refinement in P1 gives R/Rfree of 38/41) > >- data were processed with XDS as well as Dials/Aimless > >- the protein is generally well folded, quite stable, without any loose >ends or flexible regions > >- calculation of selfrotation functions in P21 and P21221 gives peak at >90dg (kappa=180dg) > >Anyone an idea what could be going on or how to solve that? > > >Thanks a lot in advance! > >Sabine
