I am working on a protein for last so many years and for which i have got crystal now in a tray which i kept 1 years ago. It diffracts well and resolution is 2.2A, which is good. 

I indexed in HKL2000, mosflm and automar and it shows P21 space group in all data reduction packages. But when I tried using molrep or phaser then I do not get any solution. The sequence of my protein is having  46% identity with other available crystal structure.

Also when I tried to get matthews coffecient, it calculates its molecular mass less ( about 35 kDa) than which should be (original 54kDa) with solvent content 47%.

I have also run the silver staining gel of the protein which contained crystal that shows about 45 kD protein band which is 10 less than the original.  Also I tried to run gel on crystal but it did not give anything as it was a small crystal. 

I have tried all combinations of the search model and tried to break available pdb many ways to make different search models but have not got any good solution. Molrep gives contrast even 10 or more but no good electron density map yet. Free R and figure of merit becomes 52% and 42% respectively in Refmac with all the solutions.  

I will highly appreciate all the suggestions for this kind of problem.

Thanks and regards

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Sonali