1 Bioc585 2008 Exercise 3 – Answers (10 points) Homework 3 (10 points) (1) Describe the electron density for Lys 81 before and after model building and refinement. Why are the maps different after model building? Include a picture of the final 2Fo-Fc (FWT) electron density map (obtained by selecting “Accessories > Take Screenshot” and pasting the image into a program such as WORD). A large positive peak (green) in the Fo-Fc map indicates a missing atom, and a negative peak (red) indicates a misplaced nitrogen. After moving the lysine nitrogen from the negative to the positive peak position and refining, the density matches the model well, indicating correct placement. (2) Describe the electron density for Ser73 before and after changing from Cys and refining. Why are the maps different? Include a picture of the final 2Fo-Fc (FWT) electron density map. There is a very large negative peak on the sulfur atom, indicating the cys to ser mutation is in place. A smaller positive peak nearby suggests two positions for the side chain. Modeling Ser 73 in two positions and refining yields a map without error for residue, indicating good agreement between model and crystal.2 (3) Describe the electron density for Cys32 before and after omitting and refining. Why are the maps different? Include a picture of the final Fo-Fc (DELFWT) electron density map and describe its significance. Before omitting, Cys 32 had moved into position for disulfide linkage during refinement. The 2Fo-Fc electron density matched the model well and only small Fo-Fc peaks remained. After omitting, density for Cys 32 appears in both the positive Fo-Fc map and the 2Fo-Fc map, indicating the correct placement for the residue in the crystal. Leaving the electrons for Cys 32 out of the model leads to the large positive Fo-Fc
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