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
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http://wwwuser.cnb.csic.es/~mjvanraaij Editor of Acta Crystallographica F, Structural Biology CommunicationsOn 19 Sep 2017, at 16:01, Satvik Kumar <[log in to unmask]> wrote:<Monomer_searchmodel.pdf><SatvikThanks,Please share your thoughts.Is my space group correct? Do I need to reexamine the space group even though the probability is high?I have pasted the pointless output to provide more information.Hello,Thanks everyone for your explanations.
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 0.48respectively. 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.
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?On Mon, Sep 18, 2017 at 7:36 PM, Eleanor Dodson <[log in to unmask]> wrote:EleanorThen look at the maps and see if there are obvious corrections to be made..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 - re PHASER. The packing rejection criteria may be set too severely - that seems the case for your solution.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.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..ways of being misled are:Is the space group correct?You need to provide a bit more information.First of all about the data processing..On 18 September 2017 at 14:59, Satvik Kumar <[log in to unmask]> wrote: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?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.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?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.
Can anyone please explain the meaning of the warning.
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,SatvikDimer_searchmodel.pdf>