Were the shares and property sold from within the estate or after they were transferred into the names of you and your sister and then sold?
If you had sold the shares and property from within the estate, there would only be one CGT exemption for the estate provided the disposals occurred in the tax year of death or either of the next two tax years. The gain would then have been disclosed in the estate tax return and the CGT paid by the estate.
You appear to have sold the assets after putting them into your name only and so you may have trouble with HMRC convincing them that you owned them jointly with your sister. The money really should not be in the estate any longer. The tax liabilities are yours, not the estate's. You and your sister need to disclose your respective shares of the gain in personal tax returns for the tax year in which they were sold. You can register to do that here if you are not already within the self-assessment system.
I hope thish helps but let me know if you have any further questions.