Comment on Three X-ray Crystal Structure Papers

Stanfield, Robyn L.; Pozharski, Edwin; Rupp, Bernhard

doi:10.4049/jimmunol.1501343

Cited by 11 publications

(15 citation statements)

References 18 publications

(17 reference statements)

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“…In fact, the challengers confirmed the correctness of the electron density for the bound ligand and also used the aforementioned arguments regarding plasticity while interpreting antibody glycosylation at relatively high B ‐factors and lower σ cut‐off in an independent antibody structure . They emphasized that the difference electron density omit maps should be viewed at a minimum of 3.0 σ because the default contour level to view such maps in Coot is 3.0 σ . However, in actual practice, crystallographers vary the σ cut‐off while interpreting difference electron density maps, often going as low as 1.5 σ .…”

Section: Challenging Publications Involving Structural Datamentioning

confidence: 93%

“…Analysis of such loop regions or bound ligands both in terms of their B-value profiles can often provide useful insights. It has been suggested recently, that in the case of ligand bound protein structures, differences in the B-factors of the ligand and the protein imply that the ligand is not bound to the protein (22). This contention is basically erroneous as there are a number of situations wherein the B-factors of the ligand and the protein can be dissimilar.…”

Section: B-factorsmentioning

confidence: 99%

“…For example, the Fo-Fc electron density maps for 2J9N and 3LK0, two structures from the challengers themselves, do not show clear density for the modeled ligands at 3r cut-off as shown in Figure 1 (6,7). Additionally, it was emphasized that the overall B factors of neighboring components in a crystal structure cannot differ drastically (22). However, the B values of the ligands in the structures 2J9N, 3LK0, 3LK1 and 3KL5 are very high compared to those of interacting amino acid residues of corresponding proteins (6,7).…”

Section: Iubmb Lifementioning

confidence: 99%

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Macromolecular structures: Quality assessment and biological interpretation

Salunke

Nair

2017

IUBMB Life

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Structure determination using X-ray crystallography involves collection of diffraction data, determination of initial phases followed by iterative rounds of model building and crystallographic refinement to improve the phases and minimize the differences between calculated and observed structure factors. At each of these stages, a variety of statistical filters exist to ensure appropriate validation. Biologically important observations often come from interpretations of signals that need to be carefully deciphered from noise, and therefore human intervention is as important as the automated methods and filters. Currently, all structural data are deposited in the Protein Data Bank (PDB), and this repository is continuously evolving to incorporate new developments in macromolecular crystallography. The journals that publish data arising from structural studies modulate their policies to take cognizance of new improved methodologies. Together, the PDB and journals have evolved an accepted protocol to ensure the integrity of crystallographic results. As a result, the quality of available data and associated interpretations have improved over the years. Typically, if there are differences regarding the mechanism of action of a protein revealed by crystallography then new experiments are carried out to provide further evidence for or against a particular hypothesis. Hence, the scientific systems in structural biology are robust and to a large extent capable of correcting any errors in interpretation of structural results. However, this process is hindered by spurious challenges to published research, based on misuse of validation mechanisms. Such activities are counterproductive and will cause damage to the field of structural biology. © 2017 IUBMB Life, 69(8):563-571, 2017.

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Section: Challenging Publications Involving Structural Datamentioning

confidence: 93%

Section: B-factorsmentioning

confidence: 99%

Section: Iubmb Lifementioning

confidence: 99%

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Macromolecular structures: Quality assessment and biological interpretation

Salunke

Nair

2017

IUBMB Life

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“…These studies involved structures of Fab fragments of antibodies with the low-affinity peptides, which were obtained through the refinement procedures outlined in the Introduction. These studies were questioned by a group of people who seem to be incapable of dealing with challenging datasets (Stanfield et al, 2016a&b). In spite of adequately responding to all the questions raised and the journal closing the subject by publishing their queries and our rebuttals (Salunke et al, 2016 a&b), the group did not stop misrepresenting our data in different ways.…”

Section: Spurious Challengesmentioning

confidence: 97%

“…Recently, it has been suggested that differences in the B-factors of the ligand and the protein imply that the ligand is not bound to the protein (Stanfield et al, 2016a). This contention is basically erroneous as there are a number of situations wherein the B-factors of the ligand and the protein can be dissimilar.…”

Section: B-factorsmentioning

confidence: 99%

Analysis of the Quality of Macromolecular Structures

Salunke

2017

Preprint

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Structure determination utilizing X-ray crystallography involves collection of diffraction data, determination of initial phases followed by iterative rounds of model building and crystallographic refinement to improve the phases and minimize the differences between calculated and observed structure factors. At each of these stages, a variety of statistical filters exist to ensure appropriate validation. Biologically important observations often come from interpretations of signals that need to be carefully deciphered from noise and therefore human intervention is as important as the automated filters. Currently, all structural data are deposited in the Protein Data Bank and this repository is continuously evolving to incorporate possible new improvements in macromolecular crystallography. The journals that publish data arising from structural studies modulate their policies to take cognizance of new improved methodologies. The PDB and journals have evolved an accepted protocol to ensure the integrity of crystallographic results. As a result, the quality of available data and interpretations are becoming better over the years. However, there have been periodic efforts by some individuals who misuse validation mechanisms to selectively target published research through spurious challenges. These actions do more harm to the field of structural biology and runs counter to their claim to cleanse the system. The scientific systems in structural biology are robust and capable of self-correction and unwarranted vigilantism is counterproductive.

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Scientific Discoveries: Real and Imagined

Franzen

2021

University Responsibility for the Adjudication of Research Misconduct

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Comment on Three X-ray Crystal Structure Papers

Cited by 11 publications

References 18 publications

Macromolecular structures: Quality assessment and biological interpretation

Macromolecular structures: Quality assessment and biological interpretation

Analysis of the Quality of Macromolecular Structures

Scientific Discoveries: Real and Imagined

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