wwPDB validation report of PDB entry 4IHI

Delta-1-pyrroline-5-carboxylate dehydrogenase

PROBABLE PYRROLINE-5-CARBOXYLATE DEHYDROGENASE ROCA

HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. STRUCTURE CONSISTS IN AN ARRANGEMENT OF ORDERED AND DISORDERED LAYERS RESULTING IN GAPS BETWEEN ORDERED MOLECULES. ALTHOUGH NO MOLECULES ARE MODELLED WITHIN THIS EMPTY LAYER, MAD DATA FROM SEMET-PRUA CRYSTALS INDICATES THAT PROTEIN ELECTRON DENSITY EXISTS WITHING THESE GAPS AND SUGGESTS A MOTION OF THE ENTIRE LAYER.

Delta-1-pyrroline-5-carboxylate dehydrogenase (E.C.1.5.1.12)
Crystal structure of the Delta-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis bound with NAD

The analyses of the Patterson function reveals a significant off-origin peak that is 34.83 % of the origin peak, indicating pseudo-translational symmetry. The chance of finding a peak of this or larger height by random in a structure without pseudo-translational symmetry is equal to 6.4136e-04. The detected translational NCS is most likely also responsible for the elevated intensity ratio. See the relevant section of the logfile for more details.

20191225.v01 (using entries in the PDB archive December 25th 2019)

structure factor analysis and validation

geometric validation package for ligand chemistry in protein x-ray structures