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

By Randy J. Read, Paul D. Adams, W. B. Arendall, A. Brunger, P. Emsley, Robbie P. Joosten, Gerard J. Kleywegt, Eugene Krissinel, Thomas Lütteke, Zbyszek Otwinowski and 7 more. 2011

445 citations recorded by the source corpus.

Summary This 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.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, background): “Ramachandran backbone scores use six ’, distributions that have quite different outlier contours: general, Ile/Val, Gly, pre-Pro, trans-Pro and cis-Pro (Read et al., 2011).”
Real-space refinement in PHENIX for cryo-EM and crystallography (2018, background): “2.3 Evaluation o f refinement progress and results 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.…”
ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps (2018, methodology): “All statistics other than EM model– map correlation were gathered from the wwPDB validation reports (Read et al., 2011); the latter were gathered from a previous analysis (Afonine et al., 2018).”
Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive (2017, background): “Initially, the wwPDB X-ray VTF made recommendations on how best to validate crystallographic data [22].”
The rate of cis-trans conformation errors is increasing in low-resolution crystal structures. (2015, background): “…menu option to manually check for cis-peptide bonds, neither PHENIX (Adams et al., 2010), MolProbity (Chen et al., 2010) nor the automated Protein Data Bank (PDB) validation tools (Read et al., 2011) provide a report on cis bonds in their standard workflow, leading to these errors going unnoticed.”
From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation (2018, background): “Validation of atomic models is now routine in macromolecular crystallography and is an integral part of structure submission to the Protein Data Bank (Read et al., 2011; Gore et al., 2017).”
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop (2015, unknown): “The wwPDB X-ray Validation Task Force (VTF) made detailed recommendations on how to best validate structures determined by X-ray crystallography (Read et al., 2011).”
MolProbity’s Ultimate Rotamer-Library Distributions for Model Validation (2016, background): “Early such distributions were binned (often at ≥ 10◦) [18], but recent ones use smooth contour surfaces, scored by what percent of the reference data lies outside that contour [1, 26].”
Using Rosetta for RNA homology modeling (2019, background): “These errors are particularly pervasive for coordinates deposited before 2014, after which the PDB began its new deposition and validation system (Chou, Echols, Terwilliger, & Das, 2016; Chou, Sripakdeevong, Dibrov, Hermann, & Das, 2013; Keating & Pyle, 2012; Read et al., 2011; Wang et al., 2008).”