ArticleActa crystallographica. Section D, Structural biology2019
Analysis and validation of macromolecular B values.
Article in Acta crystallographica. Section D, Structural biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed.
- Confidence-guided cryo-EM map optimisation with LocScale-2.0.Nature communications · 2026Article
- Measurement of atomic scattering factors by cryoelectron microscopy.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Probing the modulation of enzyme kinetics by multi-temperature, time-resolved serial crystallography.Nature communications · 2025Article
- Useful experimental aspects of small-wedge synchrotron crystallography for accurate structure analysis of protein molecules.Acta crystallographica. Section D, Structural biology · 2025Article
- Doses for X-ray and electron diffraction: New features in RADDOSE-3D including intensity decay models.Protein science : a publication of the Protein Society · 2024Article
- Using graphlet degree vectors to predict atomic displacement parameters in protein structures.Acta crystallographica. Section D, Structural biology · 2023Article
- Toward Real Real-Space Refinement of Atomic Models.International journal of molecular sciences · 2022Article
- Tyrosine 121 moves revealing a ligandable pocket that couples catalysis to ATP-binding in serine racemase.Communications biology · 2022Article
- Quantifying and comparing radiation damage in the Protein Data Bank.Nature communications · 2022Article
- B-factor accuracy in protein crystal structures.Acta crystallographica. Section D, Structural biology · 2022Article
- A method for intuitively extracting macromolecular dynamics from structural disorder.Nature communications · 2021Article
- Article
- The accuracy of protein models automatically built into cryo-EM maps with ARP/wARP.Acta crystallographica. Section D, Structural biology · 2021Article
- Article
- Local and global analysis of macromolecular atomic displacement parameters.Acta crystallographica. Section D, Structural biology · 2020Article
- Crystallization and structure of ebselen bound to Cys141 of human inositol monophosphatase.Acta crystallographica. Section F, Structural biology communications · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
This paper describes a global analysis of macromolecular B values. It is shown that the distribution of B values generally follows the shifted inverse-gamma distribution (SIGD). The parameters of the SIGD are estimated using the Fisher scoring technique with the expected Fisher information matrix. It is demonstrated that a contour plot based on the parameters of the SIGD can play a role in the validation of macromolecular structures. The dependence of the peak-height distribution on resolution and atomic B values is also analysed. It is demonstrated that the B-value distribution can have a dramatically different effect on peak heights at different resolutions. Consequently, a comparative analysis of the B values of neighbouring atoms must account for resolution. A combination of the SIGD, peak-height distribution and outlier detection was used to identify a number of entries from the PDB that require attention. It is also shown that the presence of a multimodal B-value distribution often indicates that some loops or parts of the molecule have either been mismodelled or have dramatically different mobility, depending on their environment within the crystal. These distributions can also indicate the level of sharpening/blurring used before atomic structure refinement. It is recommended that procedures such as sharpening/blurring should be avoided during refinement, although they can play important roles in map visualization and model building.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.