wwPDB validation report of PDB entry 3RJW

Histone-lysine N-methyltransferase EHMT2

Euchromatic histone-lysine N-methyltransferase 2, HLA-B-associated transcript 8, Histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, Lysine N-methyltransferase 1C, Protein G9a

Restraints for the refinement of the ligand CIQ were prepared using the prodrg server. WEAK ELECTRON DENSITY FOR THE QUINAZOLINE SUBSTITUENTS prevents UNAMBIGUOUS ASSIGNMENT OF THEIR ROTAMERIC STATES. Model geometry was validated periodically on the molprobity server. Coot was used for interactive model re-building. Non-crystallographic symmetry restraints where applied with the autobuster -autoncs switch. Coinciding with random selection of "free" reflections for cross-validation, these restraints may have introduced additional bias and disproportionately reduced the "free" residual.

Histone-lysine N-methyltransferase EHMT2 (E.C.2.1.1.43)
Crystal structure of histone lysine methyltransferase g9a with an inhibitor

The analyses of the Patterson function reveals a significant off-origin peak that is 29.53 % 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 1.5263e-03. The detected translational NCS is most likely also responsible for the elevated intensity ratio. See the relevant section of the logfile for more details.

structure factor analysis and validation

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

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