Sequence assignment validation in protein crystal structure models with checkMySequence

Abstract

Sequence register shifts remain one of the most elusive errors in experimental macromolecular models. They may affect model interpretation and propagate to newly built models from older structures. In a recent publication I have shown that register shifts in cryo-EM models of proteins can be detected using a systematic re-assignment of short model fragments to the target sequence. Here, I show that the same approach can be used to detect register shifts in crystal structure models using standard, model-bias corrected electron-density maps. I describe in detail five register shift errors detected using the method in models deposited in the PDB. SynopsisI show that checkMySequence, an automated method for validating sequence assignment in cryo-EM structures of proteins, can be used for validating crystal structure models.