Abstract
Background: As more protein atomic structures are determined from cryo-electron microscopy (cryo-EM) density maps, validation of such structures is an important task. Methods: We applied a histogram-based outlier score (HBOS) to six sets of cryo-EM atomic structures and five sets of X-ray atomic structures, including one derived from X-ray data with better than 1.5 Å resolution. Cryo-EM data sets contain structures released by December 2016 and those released between 2017 and 2019, derived from resolution ranges 0–4 Å and 4–6 Å respectively. Results: The distribution of HBOS values in five sets of X-ray structures show that HBOS is sensitive distinguishing sets of X-ray structures derived from different resolution ranges-higher than 1.5 Å, 1.5–2.0 Å, 2.0–2.5 Å, 2.5–3.0 Å, and 3.0–3.5 Å. The overall quality of cryo-EM structures is likely improved, as shown in a comparison of cryo-EM structures released before the end of 2016, those between 2017 and 2018, and those between 2018 and 2019. Our investigation shows that leucine (LEU) has a significantly higher rate of HBOS outliers than that of the reference data set (X-ray-1.5) and of other residue types in the cryo-EM data sets. HBOS was able to detect outliers for those residues that are currently marked as green in PDB validation reports. Conclusions: The HBOS profile of a dataset is a potential method to characterize the overall structural quality of the set. Residue LEU deserves special attention since it has a significantly higher HBOS outlier rate in sets of cryo-EM structures and those X-ray structures derived from X-ray data of lower than 2.5 Å resolutions. Most HBOS outlier residues from the EM-0-4-2019 set are located on loops for most types of residues.
Highlights
Cryo-electron microscopy is an essential method to determine three-dimensional atomic structures of proteins and some RNA and DNA molecules [1,2,3,4,5,6,7]
Outlier rate in sets of cryo-electron microscopy (cryo-EM) structures and those X-ray structures derived from X-ray data of lower than 2.5 Å resolutions
Most histogram-based outlier score (HBOS) outlier residues from the EM-0-4-2019 set are located on loops for most types of residues
Summary
Cryo-electron microscopy (cryo-EM) is an essential method to determine three-dimensional atomic structures of proteins and some RNA and DNA molecules [1,2,3,4,5,6,7]. As of January 08, 2020, the Worldwide Protein Data Bank (wwPDB) (https://www.wwpdb.org/) contains entries of atomic structures derived from the cryo-EM technique, about 2.6% of 159,230 structures in wwPDB [10,11]. As more protein atomic structures are determined from cryo-electron microscopy (cryo-EM) density maps, validation of such structures is an important task. Methods: We applied a histogram-based outlier score (HBOS) to six sets of cryo-EM atomic structures and five sets of X-ray atomic structures, including one derived from X-ray data with better than 1.5 Å resolution. HBOS was able to detect outliers for those residues that are currently marked as green in PDB validation reports
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