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 Diffraction of Biological Samples01:10

X-ray Diffraction of Biological Samples

X-ray diffraction or XRD is an analytical tool that utilizes X-rays to study ordered structures such as crystalline organic and inorganic samples, polycrystalline materials, proteins, carbohydrates, and drugs.
According to Bragg's law, when X-rays strike the sample positioned on a stage, the rays are  scattered by the electron clouds around the sample atoms. The  X-ray diffraction or scattering is caused by constructive interference of the X-ray waves that reflect off the internal crystal...
X-ray Crystallography02:18

X-ray Crystallography

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...
Super-resolution Fluorescence Microscopy01:37

Super-resolution Fluorescence Microscopy

Super-resolution fluorescence microscopy (SRFM) provides a better resolution than conventional fluorescence microscopy by reducing the point spread function (PSF). PSF is the light intensity distribution from a point that causes it to appear blurred. Due to PSF, each fluorescing point appears bigger than its actual size, and it is the PSF interference of nearby fluorophores that causes the blurred image. Various approaches to achieving higher resolution through SRFM have recently been developed.
Electron Microscope Tomography and Single-particle Reconstruction01:07

Electron Microscope Tomography and Single-particle Reconstruction

Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
Electron tomography can be performed either in TEM or STEM (scanning transmission...

You might also read

Related Articles

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

Sort by
Same author

Diversity-driven biochemical survey reveals widespread dimerization throughout the rubisco superfamily.

Nature communications·2026
Same author

The NMR Exchange Format (NEF): Specification and Applications.

bioRxiv : the preprint server for biology·2026
Same author

<i>pyDiSCaMB</i>: enabling the use of multipolar scattering factors in <i>Phenix</i>.

Journal of applied crystallography·2026
Same author

Variable Resolution Maps (VRM) in CCTBX and Phenix: Accounting For Local Resolution In cryoEM.

bioRxiv : the preprint server for biology·2026
Same author

The Untangle Challenge for accurate ensemble models.

bioRxiv : the preprint server for biology·2026
Same author

Validated ligand geometries for macromolecular refinement restraints and molecular-mechanics force fields.

Acta crystallographica. Section D, Structural biology·2026

Related Experiment Video

Updated: Jul 10, 2026

An All-in-one Sample Holder for Macromolecular X-ray Crystallography with Minimal Background Scattering
07:55

An All-in-one Sample Holder for Macromolecular X-ray Crystallography with Minimal Background Scattering

Published on: July 6, 2019

On macromolecular refinement at subatomic resolution with interatomic scatterers.

Pavel V Afonine1, Ralf W Grosse-Kunstleve, Paul D Adams

  • 1Lawrence Berkeley National Laboratory, One Cyclotron Road, BLDG 64R0121, Berkeley, CA 94720, USA. pafonine@lbl.gov

Acta Crystallographica. Section D, Biological Crystallography
|November 17, 2007
PubMed
Summary

Accurate electron density mapping in crystals needs advanced models. A new mixed atomic model offers results comparable to complex multipolar models, even with limited data.

More Related Videos

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering
07:19

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Published on: November 5, 2018

Do's and Don'ts of Cryo-electron Microscopy: A Primer on Sample Preparation and High Quality Data Collection for Macromolecular 3D Reconstruction
09:25

Do's and Don'ts of Cryo-electron Microscopy: A Primer on Sample Preparation and High Quality Data Collection for Macromolecular 3D Reconstruction

Published on: January 9, 2015

Related Experiment Videos

Last Updated: Jul 10, 2026

An All-in-one Sample Holder for Macromolecular X-ray Crystallography with Minimal Background Scattering
07:55

An All-in-one Sample Holder for Macromolecular X-ray Crystallography with Minimal Background Scattering

Published on: July 6, 2019

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering
07:19

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Published on: November 5, 2018

Do's and Don'ts of Cryo-electron Microscopy: A Primer on Sample Preparation and High Quality Data Collection for Macromolecular 3D Reconstruction
09:25

Do's and Don'ts of Cryo-electron Microscopy: A Primer on Sample Preparation and High Quality Data Collection for Macromolecular 3D Reconstruction

Published on: January 9, 2015

Area of Science:

  • Crystallography
  • Materials Science
  • Computational Chemistry

Background:

  • Accurate electron density distribution in molecular crystals at subatomic resolution requires models beyond independent spherical atoms.
  • The multipolar model is a conventional tool, but insufficient experimental data limits its refinement, especially at resolutions of 0.8-1.0 Å.
  • Simpler models are needed for accurate electron density studies when data is limited.

Purpose of the Study:

  • To evaluate a simpler, mixed atomic model for electron density refinement in crystallography.
  • To compare the performance of the mixed model against conventional and multipolar models.
  • To demonstrate the applicability of the mixed model to both small molecules and macromolecules.

Main Methods:

  • Development and application of a mixed atomic model, combining independent spherical atoms with additional scatterers for bonding effects.
  • Refinement of the mixed model using the phenix.refine module within the PHENIX package.
  • Testing the model on several benchmark datasets of small molecules and macromolecules.

Main Results:

  • The mixed model yielded results comparable in quality to multipolar refinement.
  • The mixed model significantly outperformed conventional atomic models.
  • Successful application of the mixed model to diverse crystallographic datasets, including macromolecules.

Conclusions:

  • The proposed mixed atomic model provides a viable and effective alternative for accurate electron density distribution studies.
  • This model offers a practical solution for refinement when experimental data is insufficient for full multipolar models.
  • The phenix.refine implementation facilitates the application of this advanced modeling technique in crystallography.