Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

X-ray Crystallography02:18

X-ray Crystallography

24.5K
The size of the unit cell and the arrangement of atoms in a crystal may be determined from measurements of the diffraction of X-rays by the crystal, termed X-ray crystallography.
Diffraction
Diffraction is the change in the direction of travel experienced by an electromagnetic wave when it encounters a physical barrier whose dimensions are comparable to those of the wavelength of the light. X-rays are electromagnetic radiation with wavelengths about as long as the distance between neighboring...
24.5K
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

45.1K
Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
45.1K
Improving Translational Accuracy02:07

Improving Translational Accuracy

12.0K
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
12.0K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

What Is the Crystallographic Resolution of Structural Models of Proteins Generated with AlphaFold2?

ACS chemical biology·2024
Same author

Location of S-nitrosylated cysteines in protein three-dimensional structures.

Proteins·2023
Same author

Chalcogen bonds formed by protein sulfur atoms in proteins. A survey of high-resolution structures deposited in the protein data bank.

Journal of biomolecular structure & dynamics·2022
Same author

Interplay between hydrogen and chalcogen bonds in cysteine.

Proteins·2022
Same author

Survey of the Intermolecular Disulfide Bonds Observed in Protein Crystal Structures Deposited in the Protein Data Bank.

Life (Basel, Switzerland)·2022
Same author

Random sampling of the Protein Data Bank: RaSPDB.

Scientific reports·2021

Related Experiment Video

Updated: Oct 8, 2025

Crystallization and Structural Determination of an Enzyme:Substrate Complex by Serial Crystallography in a Versatile Microfluidic Chip
10:45

Crystallization and Structural Determination of an Enzyme:Substrate Complex by Serial Crystallography in a Versatile Microfluidic Chip

Published on: March 20, 2021

8.5K

B-factor accuracy in protein crystal structures.

Oliviero Carugo1

  • 1Department of Chemistry, University of Pavia, Viale Taramelli 12, I-27100 Pavia, Italy.

Acta Crystallographica. Section D, Structural Biology
|January 4, 2022
PubMed
Summary

The accuracy of B factors in protein crystal structures is limited, with large errors comparable to two decades ago. Normalizing B factors is essential for comparing protein dynamics across different structures.

Keywords:
B factorsaccuracynormal probability plotprotein crystal structuresvalidation

More Related Videos

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules
07:11

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

Published on: March 22, 2019

7.0K
Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques
08:58

Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques

Published on: July 5, 2018

12.8K

Related Experiment Videos

Last Updated: Oct 8, 2025

Crystallization and Structural Determination of an Enzyme:Substrate Complex by Serial Crystallography in a Versatile Microfluidic Chip
10:45

Crystallization and Structural Determination of an Enzyme:Substrate Complex by Serial Crystallography in a Versatile Microfluidic Chip

Published on: March 20, 2021

8.5K
Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules
07:11

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

Published on: March 22, 2019

7.0K
Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques
08:58

Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques

Published on: July 5, 2018

12.8K

Area of Science:

  • Biochemistry
  • Structural Biology
  • Crystallography

Background:

  • B factors in protein crystal structures quantify atomic motion and disorder.
  • Previous estimates of B factor error are decades old.
  • B factors are influenced by factors beyond local atomic movement.

Purpose of the Study:

  • To determine the accuracy of B factors in protein crystal structures.
  • To assess the magnitude of B factor errors.
  • To evaluate the consistency of B factor accuracy over time.

Main Methods:

  • Comparing B factors of identical atoms across multiple independent crystal structures of Gallus gallus lysozyme.
  • Analyzing B-factor absolute differences.
  • Utilizing normal probability plots to assess B factor errors.

Main Results:

  • Estimated B factor errors are substantial, approximately 9 Ų for ambient-temperature structures and 6 Ų for low-temperature structures.
  • These error magnitudes are comparable to those estimated 20 years ago.
  • B factor accuracy is significantly affected by crystal defects, disorder, and diffraction data quality.

Conclusions:

  • B factor accuracy in protein crystallography remains a significant challenge.
  • Normalization of B factors is crucial for reliable comparisons of protein dynamics between structures.
  • Novel experimental and computational tools are needed to accurately disaggregate local atomic movements from other influences on B factors.