A New Generation of Crystallographic Validation Tools for the Protein Data Bank

Abstract

SummaryThis report presents the conclusions of the X-ray Validation Task Force of the worldwide Protein Data Bank (PDB). The PDB has expanded massively since current criteria for validation of deposited structures were adopted, allowing a much more sophisticated understanding of all the components of macromolecular crystals. The size of the PDB creates new opportunities to validate structures by comparison with the existing database, and the now-mandatory deposition of structure factors creates new opportunities to validate the underlying diffraction data. These developments highlighted the need for a new assessment of validation criteria. The Task Force recommends that a small set of validation data be presented in an easily understood format, relative to both the full PDB and the applicable resolution class, with greater detail available to interested users. Most importantly, we recommend that referees and editors judging the quality of structural experiments have access to a concise summary of well-established quality indicators.

Integrative structure and functional anatomy of a nuclear pore complex

“…Moreover, our sampling was not completely stochastic because it proceeded in two steps, the first of which prepared the starting configuration for the second step. As a result, the actual structure precision might be worse 134–137 than the estimated 9 Å.…”

The Protein Data Bank archive as an open data resource

“…These structures, along with an ongoing concern for ensuring the quality of the data archive [25], motivated the wwPDB to convene an X-ray Validation Task Force (VTF) consisting of scientists with expert knowledge of crystallographic methods and validation procedures [26]. The X-ray VTF was charged with recommending best practices for validation that the wwPDB could then implement in its data-processing pipeline [27].…”

Real-space refinement in Phenix for cryo-EM and crystallography

“…It is recognized that model validation (for example Branden & Jones, 1990;Read et al, 2011;Wlodawer & Dauter, 2017) is a critical step in structure determination and a number of corresponding tools have been developed in crystallography (e.g. Chen et al, 2010;Gore et al, 2012;Young et al, 2017, and references therein) and some in cryo--EM studies (see for example, Henderson et al, 2012;Tickle, 2012;Barad et al, 2015;Pintilie et al, 2016;Joseph et al, 2017, Afonine et al, 2018.…”