Structure validationStructure validation

Everything that can go wrong, will go Everything that can go wrong, will go wrong. wrong.

Everything that could go wrong has gone Everything that could go wrong has gone wrong.wrong.

Especially with something as complicated Especially with something as complicated as a protein structure.as a protein structure.

What does WHAT_CHECK What does WHAT_CHECK check?check?

Administrative errors.Crystal-specific errors.NMR-specific errors.Really wrong things.Improbable things.Things worth looking at.Ad hoc things.www.cmbi.kun.nl/gv/pdbreport/www.cmbi.kun.nl/gv/servers/

How wrong is wrong?How wrong is wrong?

Growth of the number of Growth of the number of avoidable four sigmasavoidable four sigmas

10^7

10^6

97 01 97 01

PDB FILES ERRORS

3K

15K

What did we find?What did we find?

Trp with 90 degree angle between rings.His with two N-s in side chain bound.Cys-Cys bridge with one S.Asp and Leu conformation swapped.Lysine neutral at pH 5.5.A molecule consisting of 628 waters.One molecule with four names.One name used for four molecules.Thr with wrong C-beta chirality.Missed cis-peptide bonds.Alternate conformations are random.

What did we find?What did we find?

B-factor refinement in TNT is random.His in X-plor is always positive.Asp in CNS has protons backwards.Planarity too relaxed in X-plor, etc.Many waters placed at C-alpha.C-terminal oxygen in middle of chain.Non-crystallographic symmetry is real.Strand goes through core of helix.Hexamer presented as monomer.Occupancies above 1.0.Etc., Etc., Etc., Etc., Etc., Etc., Etc., Etc., Etc., Etc., Etc.,…………………………….

Close to 1.000.000 timesClose to 1.000.000 times

About 50 timesAbout 50 times

Your best check:Your best check:

ConclusionsConclusions

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).Often we can detect that something is rotten without knowing what is rotten.

WHAT_CHECK by:WHAT_CHECK by:

Rob Hooft