1. Structure validation
Everything that can go wrong, will go wrong, especially with things as complicated as protein structures.

2. What is real?

3. What is real?
ATOM 1 N LEU
ATOM 2 CA LEU
ATOM 3 C LEU
ATOM 4 O LEU
ATOM 5 CB LEU
ATOM 6 CG LEU
ATOM 7 CD1 LEU
ATOM 8 CD2 LEU

4. X-ray

5. X-ray

6. X-ray
‘FFT-inv’
FFT-inv

7. X-ray R-factor 2
Error = Σ w.(obs-calc)
R-factor = Σ w.|obs-calc|

8. X-ray resolution

9. NMR versus X-ray ‘Error’ 1-2 Å 0.1-0.5 Å Mobility yes not really
Crystal artefacts no yes
Material needed 20 mg 1 mg
Cost of hardware 4 M Euro near infinite (share)
Drug design no almost
Better combine and use the best of both worlds.

10. Why ?
Why does a sane (?) human being spend fourteen years to search for millions of errors in the PDB?

11. Because: Everything we know about proteins comes from PDB files.
If a template is wrong the model will be wrong.
Errors become less dangerous when you know about them.

12. What do we check? Administrative errors. Crystal-specific errors.
NMR-specific errors.
Really wrong things.
Improbable things.
Things worth looking at.
Ad hoc things.

13. 1FCC

14. Smile or cry?
A 5RXN
B 7GPB
C 1DLP
D 1BIW 2.5

15. X-ray specific

16. Little things hurt big

17. Contact Probability

18. Contact Probability

19. DACA

20. DACA

21. DACA

22. DACA

23. DACA

24. Contact probability box

25. His, Asn, Gln ‘flips’

26. Hydrogen bond network

27. Conclusions Everything that could go wrong has gone wrong.
Errors are on a ‘sliding scale’.
Error detection can detect a lot, but surely not everything (yet).

28. Acknowledgements: Rob Hooft Elmar Krieger Sander Nabuurs Chris Spronk
Robbie Joosten
Maarten Hekkelman