/It is very likely to be twinned with your true spacegroup being P6. Look at the /twinning documentation for details of twinning in P6 SGs http://www.ccp4.ac.uk/dist/html/twinning.html
It is very likely that extra density is your twin "ghost". First hint work in P6 without trying to detwin. You should get a solution with the dimer. Then try twin refinement in SHELXL - you run SHELXPRO to convert your coordinates to the SHELX style. Then add to the ins file two lines TWIN 0 1 0 1 0 0 0 0 -1 ( This gives twin law k,h,-l - the only one allowed in P6i) BASF 0.3 ( This is the twinning fraction which will be refined..) ..... DELU $C_* $N_* $O_* $S_* etc .. Eleanor Tony Hu wrote: >*** For details on how to be removed from this list visit the *** >*** CCP4 home page http://www.ccp4.ac.uk *** > > >Dear all, > >We recently collected a set of data belonging to P622 group (as far as I am >concerned), and we're trying to solve the structure using a 46% sequence >identical template with molecular replacement. But some peculiar problems >occurred during the process which is beyond our ability to solve, so I hope >someone could give us some advice. Here is the case: > >1. Data information >(1) Spacegroup: P622, Cell parameters: 147.97 A, 147.97 A, 163.47 A; 90 >degree, 90 degree, 120 degree >(2) Resolution: 2.4A, Completeness: 99.8%, Rmerge: ~0.1, Multiplicity: ~13 >(3) Data processing softwares: Mosflm and Scala. We've also processed the data >in P3 and P6 spacegroup, the data qualities were similar as the P622 one. >(4) Pseudo translation: SFcheck and molrep haven't detected any pseudo >translation. >(5) Twinning: We have tested the twinning possibility of the data integrated >and scaled in P6 spacegroup using Detwin and YEATES server. From the YEATES >server, partial merohedral twinning test results suggested a twinning fraction >of 0.46, similar as the Detwin result, while perfect merohedral twinning test >results suggested untwinned data. Sorry for my ignorance, but could our data >be a perfectly twinned P6 data? How can I find out? > >2. Template information >(1) 357 residues (359 residues for our protein), 46% identical in sequence >(2) Its biologically functioning unit is a dimer related by 2-fold axis, which >is also true for our protein as is determined by biochemical experiments. The >crystal structure of the template contains one monomer per ASU, but the >biological dimer could be reconstituted by relating two monomers via a 2-fold >crystallographic symmetry axis. > >3. Matthews coefficient test suggested two (24% probability) / three (76% >probability) monomers per ASU. > >4. MR with one monomer first >(1) Softwares tested: Molrep, Amore, Phaser, CNS, the results were similar. >(2) Cross rotation gave two obvious peaks, differed only by about 20 degrees >in alpha rotation angle. The 1st peak is much larger than the 2nd, but the gap >between the 2nd and rest of the peaks was also distinct. >(3) Translation with the 1st largest peak gave a good hit. After refining the >fitted model, we could unambiguously position our model in the clear electron >density map, including a ligand. The Rwork and Rfree were 38% and 42% >respectively. This monomer forms a biological dimer with its >crystallographically 2-fold related symmetry molecule. >(4) After observing the map, we could find a large area of unexplained >electron density suitable for another monomer but with poor constitutivity. >When we tried to find the 2nd monomer with the 2nd largest peak fixing the 1st >model, the results produced were all unacceptable because of clashes with >symmetry molecules. > >5. MR with a dimer (made by crystallographically relating two template or >refined monomers) >(1) Cross rotation gave one high peak. >(2) The models after translation were all rejected by the softwares because of >almost perfect overlap with symmetry molecules. > >Could any one give us some suggestions on what is going wrong with our >process? Where does the problem lie? Is it space group, twinning data, >pseudo-translation or something else of the data? > >Thanks in advance! > >Tiancen Hu >Shanghai Institute of Materia Medica >Shanghai 201203 >P.R. China > > > > > > >
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