Answer from Ronan Keegan:
he cell dimensions are very suspicious, but try merging the two sets of data to see if they really are the same - you can do that best from the integrated data sets, or just compare the Riso between the two sets of amplitudes. I think there is a web server at CCP4 SIMBAD which searches to see if your data could be from one of the common contaminates of crystallisation. Ronan Keegan <ronan.kee...@stfc.ac.uk> 11:08 (1 hour ago) to me Hi Eleanor, Yes this is true, about the SIMBAD server. You can access it from here: https://www.ccp4.ac.uk/testserv/ You'll need to make an account and SIMBAD is the final program in the list. It will test for lattice matches, contaminants and then try every (non-redundant) domain in the PDB according to the MoRDa database (about 85000 domains). It can take a few hours to run. Best wishes, Ronan On 17 June 2017 at 10:52, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > The cell dimensions are very suspicious, but try merging the two sets of > data to see if they really are the same - you can do that best from the > integrated data sets, or just compare the Riso between the two sets of > amplitudes. > I think there is a web server at CCP4 SIMBAD which searches to see if your > data could be from one of the common contaminates of crystallisation. > Eleanor > > > On 17 June 2017 at 09:16, Tristan Croll <ti...@cam.ac.uk> wrote: > >> With those statistics, it seems most probable that these two crystals are >> the same protein. Do your two target proteins share an expression system >> and/or purification protocol that could lead to the same contaminant in >> both? If you have the resolution you could try Arcimboldo to get an initial >> solution and perhaps infer the sequence from the density. If you have >> crystals to spare you could digest one and identify it via tandem mass >> spec. You might also try ContaMiner. >> >> Good luck! >> >> Tristan >> >> >> On 2017-06-17 09:07, dongxiaofei wrote: >> >>> Dear ALL, >>> >>> I got two kinds of crystals of different proteins ,but there are many >>> similarities. >>> The shape of the crystals are similar, the cell parameters are also >>> similar : >>> protein A , 136.12 94.398 89.476 90 125.479 90 , Space group C 1 2 1 >>> and >>> protein B , 136.14 94.369 89.115 90 125.495 90 , Space group C 1 2 1. >>> >>> >>> protein A has a NMR structure ,but Rfree always high above 50% after >>> molecular replacement , protein B’s Rfree is also above 50% . >>> >>> So I am wonder if these crystals are the result of debris of proteins >>> , because the growth of the crystals needs more than half a year . I >>> am sure the two proteins are different and crystals respectively come >>> from different proteins >>> >>> Any insights will be really appreciated. >>> >>> Thanks >>> >>> Dong Xiao >>> >> >
