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 Experiment Videos

An improved phase-extension procedure for isomorphous replacement phases.

Y Vekhter1, R Miller

  • 1Department of Physics, State University of New York at Buffalo, 14260, USA. dvekhter@acsu.buffalo.edu

Acta Crystallographica. Section D, Biological Crystallography
|June 22, 2001
PubMed
Summary

A novel phase extension method improves crystallographic phase accuracy and map quality over standard solvent flattening. This technique refines protein structure determination by selecting core phases for enhanced density modification.

Related Concept Videos

You might also read

Related Articles

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

Sort by
Same author

Cutaneous T-cell lymphoma presenting as a large scalp mass.

Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery·1995
Same author

Effects of recombinant dimeric TNF receptor on human inflammatory responses following intravenous endotoxin administration.

Journal of immunology (Baltimore, Md. : 1950)·1995
Same author

Association of human herpes virus with pulmonary Kaposi's sarcoma.

Lancet (London, England)·1995
Same author

Fas (CD95) participates in peripheral T cell deletion and associated apoptosis in vivo.

International immunology·1995
Same author

Epilepsy and children's social and psychological adjustment.

Journal of health and social behavior·1995
Same author

Mental health services in Sydney nursing homes.

Australian journal of public health·1995

Area of Science:

  • Structural Biology
  • Crystallography
  • Biophysics

Background:

  • Accurate crystallographic phase determination is crucial for solving protein structures.
  • Standard solvent flattening methods can be limited by the quality of initial phase sets.

Purpose of the Study:

  • To introduce and evaluate a new phase-extension procedure for improving crystallographic phases and electron density maps.
  • To compare the performance of the new method against standard solvent flattening techniques.

Main Methods:

  • A new phase-extension procedure was developed, starting with a core subset of phases selected by phase-probability curve sharpness.
  • Phase extension was performed using solvent flattening as the density-modification procedure, gradually incorporating additional phases.
  • The method was tested on known protein structures using isomorphous replacement and single isomorphous replacement (SIR) data.

Related Experiment Videos

Main Results:

  • The new procedure yielded improved phases and maps compared to standard solvent flattening.
  • Mean phase errors were reduced by 3-9 degrees and map correlation coefficients increased by 0.05-0.18.
  • For SIR data, the lowest final mean phase errors were approximately 58 degrees with map correlation coefficients of 0.53-0.68.

Conclusions:

  • The developed phase-extension procedure offers a significant improvement over standard methods for crystallographic phase determination.
  • This technique enhances the accuracy of electron density maps, leading to better protein structure elucidation.
  • The method shows particular promise for datasets with initial phase uncertainties, such as those from SIR.