Well - you haven't said what the sequence identity between model and your protein is, nor if you have a non-crystallographic translation.
With low homology that R factor drop is acceptable and rebuilding can fix it, However if there is high homology you might expect better. But this sort of conjecture is pretty pointless - check in all orthorhombic space groups as Mark suggests. Eleanor On 19 September 2017 at 15:16, Mark J van Raaij <mjvanra...@cnb.csic.es> wrote: > With Rs of 43/48% I don't think you can be sure that your spacegroup is > right. > You should always try all the spacegroup possibilities until you get a > solution you are sure is right, i.e. that refines to Rs of around 35% or > preferably even lower. > More so in the case of screw axes, so try P222, P2122, P2212, P2221, > P21212, P21221, P22121 and P212121. Phaser can do this automatically for > you by clicking the right box. > If necessary, then try lower symmetry like P21 and perhaps P1. > Programs like Xanuda can help. > > > Mark J van Raaij > Dpto de Estructura de Macromoleculas > Centro Nacional de Biotecnologia - CSIC > calle Darwin 3 > E-28049 Madrid, Spain > tel. (+34) 91 585 4616 <+34%20915%2085%2046%2016> > http://wwwuser.cnb.csic.es/~mjvanraaij > Editor of Acta Crystallographica F, Structural Biology Communications > http://journals.iucr.org/f/ > > On 19 Sep 2017, at 16:01, Satvik Kumar <kumarsatvi...@gmail.com> wrote: > > Hello, > > Thanks everyone for your explanations. > > I have pasted the pointless output to provide more information. > > Best Solution: space group P 21 21 21 > > Laue group probability: 0.959 > > Systematic absence probability: 0.818 > > Total probability: 0.785 > > Space group confidence: 0.751 > > Laue group confidence 0.951 > > > Unit cell: 82.10 100.51 157.11 90.00 90.00 90.00 > > Also based on L-test, pointless says data does not suggest twinning. > > Yes, the R values go down when I refine in both cases. After 20 rounds of > restrained refinement using the coordinates generated by monomer as search > model, the Rwork and Rfree are 0.43 and 0.48 > > respectively. Refinement using the coordinates generated by using dimer as > search model also results in similar R values. I have attached the plots to > show that the R values indeed reduce in both cases. > > Is my space group correct? Do I need to reexamine the space group even > though the probability is high? > > If my space group is indeed correct, how do I decide whether to go ahead > with the results generated by the monomer search model or the dimer? > > Please share your thoughts. > > > Thanks, > Satvik > > On Mon, Sep 18, 2017 at 7:36 PM, Eleanor Dodson <eleanor.dod...@york.ac.uk > > wrote: > >> You need to provide a bit more information. >> >> First of all about the data processing.. >> >> Is the space group correct? >> ways of being misled are: >> Non-crystallographic translations with a shift of ~0.5 along an axis - >> say a. This will generate absences in the odd h 0 0 reflections and can >> make the space group appear to be P 21 21 21 whilst it is really P 2 21 21.. >> >> Perfect twinning can have the same effect. In an orthorhombix space group >> this can usually only occur if two axes have approximately the same length, >> but the data processing stats can indicate if that is the case. >> >> Then - re PHASER. The packing rejection criteria may be set too severely >> - that seems the case for your solution. >> >> Best check on any MR solution is: does it refine - give it 20 cycles of >> mindless refinement and see if the R and FreeR go down. >> >> Then look at the maps and see if there are obvious corrections to be >> made.. >> >> Eleanor >> >> On 18 September 2017 at 14:59, Satvik Kumar <kumarsatvi...@gmail.com> >> wrote: >> >>> Dear Crystallographers, >>> >>> I am trying to solve a structure in the space group P212121. Based on >>> Matthews coefficient, there are 4 molecules in the asymmetric unit. >>> >>> Based on my limited reading about using of Phaser, I understand that a >>> single chain should be used as search model even though many copies are >>> present in asymmetric unit. Am I correct? >>> >>> So when I use a single chain as search model and ask Phaser to search >>> for 4 molecules, Phaser identifies a single solution with a warning "The >>> top solution from a TF rescoring did not pack" and a warning "Search >>> request requires more scattering than defined in composition. Composition >>> increased to accommodate search components". But the final values reported >>> "PAK=2 >>> LLG=1065 TFZ==22.6" indicate that phaser has solved the problem. >>> >>> Can anyone please explain the meaning of the warning. >>> >>> When I inspect the arrangement of the chains (attachment), I observe >>> minimal contact between the chains and a large cavity in the center. Can a >>> crystal form this way? >>> >>> I have also tried using the dimer as search model and asking phaser to >>> search for 2 molecules. Even in this case, Phaser finds a single solution >>> but the warning and the advisory still appear as before. The numbers >>> reported reduce a bit to "PAK=1 LLG=722 TFZ==29.2". >>> >>> Please help me in understanding these results. >>> >>> Thanks, >>> Satvik >>> >>> >>> >> > <Monomer_searchmodel.pdf><Dimer_searchmodel.pdf> > > >
