ArticleActa crystallographica. Section D, Biological crystallography2012
To B or not to B: a question of resolution?
Article in Acta crystallographica. Section D, Biological crystallography, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
36 citing papers in PubMed.
- Dimerization of ADAR1 modulates site-specificity of RNA editing.Nature communications · 2024Article
- Using graphlet degree vectors to predict atomic displacement parameters in protein structures.Acta crystallographica. Section D, Structural biology · 2023Article
- Cucurbit[7]uril Enhances Distance Measurements of Spin-Labeled Proteins.Journal of the American Chemical Society · 2023Article
- Analyzing Current Trends and Possible Strategies to Improve Sucrose Isomerases' Thermostability.International journal of molecular sciences · 2023Review
- Analytic modeling of inhomogeneous-resolution maps in cryo-electron microscopy and crystallography.IUCrJ · 2022Article
- Toward Real Real-Space Refinement of Atomic Models.International journal of molecular sciences · 2022Article
- B-factor accuracy in protein crystal structures.Acta crystallographica. Section D, Structural biology · 2022Article
- Arresting the Catalytic Arginine in Chlorite Dismutases: Impact on Heme Coordination, Thermal Stability, and Catalysis.Biochemistry · 2021Article
- Local and global analysis of macromolecular atomic displacement parameters.Acta crystallographica. Section D, Structural biology · 2020Article
- Article
- Molecular determinants of vascular transport of dexamethasone in COVID-19 therapy.bioRxiv : the preprint server for biology · 2020Article
- Albumin-Based Transport of Nonsteroidal Anti-Inflammatory Drugs in Mammalian Blood Plasma.Journal of medicinal chemistry · 2020Article
- Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain.The FEBS journal · 2020Article
- Structure of a single-chain H2A/H2B dimer.Acta crystallographica. Section F, Structural biology communications · 2020Article
- A practical overview of molecular replacement: Clostridioides difficile PilA1, a difficult case study.Acta crystallographica. Section D, Structural biology · 2020Article
- Structures of Respiratory Supercomplex I+IIIMolecular cell · 2019Article
- Pyrimidine biosynthesis in pathogens - Structures and analysis of dihydroorotases from Yersinia pestis and Vibrio cholerae.International journal of biological macromolecules · 2019Article
- Review
- Analysis and validation of macromolecular B values.Acta crystallographica. Section D, Structural biology · 2019Article
- A close look onto structural models and primary ligands of metallo-β-lactamases.Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy · 2018Review
Corrections and comments
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Abstract
In choosing and refining any crystallographic structural model, there is tension between the desire to extract the most detailed information possible and the necessity to describe no more than what is justified by the observed data. A more complex model is not necessarily a better model. Thus, it is important to validate the choice of parameters as well as validating their refined values. One recurring task is to choose the best model for describing the displacement of each atom about its mean position. At atomic resolution one has the option of devoting six model parameters (a 'thermal ellipsoid') to describe the displacement of each atom. At medium resolution one typically devotes at most one model parameter per atom to describe the same thing (a 'B factor'). At very low resolution one cannot justify the use of even one parameter per atom. Furthermore, this aspect of the structure may be described better by an explicit model of bulk displacements, the most common of which is the translation/libration/screw (TLS) formalism, rather than by assigning some number of parameters to each atom individually. One can sidestep this choice between atomic displacement parameters and TLS descriptions by including both treatments in the same model, but this is not always statistically justifiable. The choice of which treatment is best for a particular structure refinement at a particular resolution can be guided by general considerations of the ratio of model parameters to the number of observations and by specific statistics such as the Hamilton R-factor ratio test.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.