PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons
E-Collection

Related Articles
Families in Gene Neighborhoods
June 2015
Expanding the Reach of SAD
April 2015
Greasing the Path for SFX
January 2015
Time-Resolved Crystallography with HATRX
December 2014
Structures Without Damage
August 2014
Error Prevention
July 2014
A Refined Refinement Strategy
May 2014
Membrane Proteome: Microcrystals Yield Big Data
April 2014
Optimizing Damage
February 2014
Getting Better at Low Resolution
January 2014
Building a Structural Library
November 2013
Drug Discovery: Identifying Dynamic Networks by CONTACT
October 2013
Microbiome: Solid-State NMR, Crystallized
September 2013
Fluorescence- and Chromatography-Based Protein Thermostability Assay
October 2012
Insert Here
October 2012
Native phasing
August 2012
Smaller may be better
April 2012
Metal mates
February 2012
Not so cool
December 2011
One from many
August 2011
Rosetta hone
July 2011
Solutions in the solution
June 2011
Beyond crystals, solutions, and powders
May 2011
Snapshot crystallography
March 2011
FERM-ly bound
February 2011
A new amphiphile for crystallizing membrane proteins
January 2011
'Super-resolution' large complexes
December 2010
Proteinase K and Digalacturonic Acid
September 2010
Some crystals like it hot
May 2010
Tips for crystallizing membrane proteins in lipidic mesophases
February 2010
Tackling the phase problem
November 2009
Crystallizing glycoproteins
September 2009
Crystals from recalcitrant proteins
August 2009
Tips for crystallizing membrane proteins
June 2009
Chaperone-assisted crystallography
March 2009
An “X-ray” ruler
January 2009
Methylation boosts protein crystallization
December 2008

Technology Topics Crystallography

A Refined Refinement Strategy

SBKB [doi:10.1038/sbkb.2014.200]
Technical Highlight - May 2014
Short description: Combinatorial use of refinement algorithms leads to improved structure determination.

Schematic illustration of the extensive combinatorial refinement procedure. Figure courtesy of Kendall Nettles.

During structure refinement, crystallographers must choose a combination of the many available refinement algorithms that leads to the highest quality structure. To achieve this, it is common to use a decision tree in which single algorithms are evaluated for their ability to improve the model. The final refinement strategy is defined by the combination of those algorithms that effectively improved the model individually. This approach assumes, however, that each algorithm is independent, and that models will not worsen over the course of refinement.

Nettles and colleagues recently tested these assumptions by developing Extensive Combinatorial Refinement (ExCoR), a combinatorial refinement approach in which 256 distinct combinations of refinement parameters and algorithms are applied in parallel to determine an ideal refinement strategy. In applying ExCoR to 53 different protein structures, the authors showed that this method can reveal improved refinement protocols for each sample—even previously refined and published structures—and can allow for the automated correction of side chains, main chains and ligands.

Although the authors expected ExCoR might reveal optimal refinement strategies that could be generally applicable to most protein structures, no single strategy consistently produced the best model. Even more surprising was the observation that, in some cases, combining two algorithms that individually made the model worse could result in a better final model. These data suggest that refinement algorithms should not be evaluated in isolation, and that refinement strategies that temporarily worsen a model may be beneficial in forcing models out of local energy minima.

ExCoR was demonstrated to improve models at all stages of the refinement process, and should aid researchers in identifying which combination of refinement algorithms will yield the best final structure. Additionally, by eliminating the need to make decisions about which refinement algorithms to use, ExCoR may provide another step toward more automated structure solution.

Timothy Silverstein

References

  1. J. C. Nwachukwu et al. Improved crystallographic structures using extensive combinatorial refinement.
    Structure. 21, 1923-1930 (2013). doi:10.1016/j.str.2013.07.025

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health