Errors

This whole course we have been looking at protein structures. We know that these structures were solved by X-ray or NMR, and we know that those are two experimental techniques; and experimental techniques have experimental errors. Consequently, all structures we have so far looked at have experimental errors. Most of those errors are small and unlikely to change the outcome of your research that is based on that structure, but some structures contain really bad problems. If that is the case it seems useful to at least know where those errors are.

Lets start with a few simple cases. We will work with the molecule hypothase. Any idea what is the function of this protein?

Figure 53. The structure of hypothase.

Get from the list of Exercise Files the following files and analyze their structures:

• hypo_bad_01.pdb
• hypo_bad_02.pdb
• hypo_bad_03.pdb
• hypo_bad_04.pdb

Each of these four structures contains one big bad error. Not a contact that is 0.5 Ångström  too short or so, but something really bad. Find in each of the structures the error, and tell me how such an error can occur.

Question 58: What is wrong with hypo_bad_01.pdb?

Question 59: What is wrong with hypo_bad_02.pdb?

Question 60: What is wrong with hypo_bad_03.pdb?

Question 61: What is wrong with hypo_bad_04.pdb?