On the need for an international effort to capture, share and use crystallization screening data

Newman, Janet; Bolton, Evan; Müller-Dieckmann, Jochen; Fazio, Vincent J.; Gallagher, D.T.; Lovell, David; Luft, Joseph R.; Peat, Thomas S.; Ratcliffe, David; Sayle, Roger A.; Snell, Edward H.; Taylor, Kerry; Vallotton, Pascal; Velanker, Sameer; Delft, Frank von

doi:10.1107/s1744309112002618

Cited by 39 publications

(45 citation statements)

References 32 publications

(35 reference statements)

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“…Exhaustive searches are simply beyond experimental reach [36]. Crystallographers have thus developed chemical screens summarizing conditions that have been previously successful.…”

Section: Diffraction and Protein Crystallizationmentioning

confidence: 99%

Soft matter perspective on protein crystal assembly

Fusco

Charbonneau

2016

Colloids and Surfaces B: Biointerfaces

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“…Exhaustive searches are simply beyond experimental reach [36]. Crystallographers have thus developed chemical screens summarizing conditions that have been previously successful.…”

Section: Diffraction and Protein Crystallizationmentioning

confidence: 99%

Soft matter perspective on protein crystal assembly

Fusco

Charbonneau

2016

Colloids and Surfaces B: Biointerfaces

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“…A successful crystallization requires a continuous monitoring of the process and a careful scoring of the results [226]. The experimental methods more frequently used in the analysis of the crystal growth experiments and in the interpretation of their results are reported in Table 4.…”

Section: Real-time Monitoring Of Crystalsmentioning

confidence: 99%

An Overview of Biological Macromolecule Crystallization

Krauss

Merlino

Vergara

et al. 2013

IJMS

123

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The elucidation of the three dimensional structure of biological macromolecules has provided an important contribution to our current understanding of many basic mechanisms involved in life processes. This enormous impact largely results from the ability of X-ray crystallography to provide accurate structural details at atomic resolution that are a prerequisite for a deeper insight on the way in which bio-macromolecules interact with each other to build up supramolecular nano-machines capable of performing specialized biological functions. With the advent of high-energy synchrotron sources and the development of sophisticated software to solve X-ray and neutron crystal structures of large molecules, the crystallization step has become even more the bottleneck of a successful structure determination. This review introduces the general aspects of protein crystallization, summarizes conventional and innovative crystallization methods and focuses on the new strategies utilized to improve the success rate of experiments and increase crystal diffraction quality.

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“…Our findings emphasize the need for an increased availability and standardization of protein crystallization datasets [8]. A richer characterization of the experimental outcomes would also extend the reliability of these models.…”

Section: Discussionmentioning

confidence: 58%

Statistical Analysis of Crystallization Database Links Protein Physico-Chemical Features with Crystallization Mechanisms

et al. 2014

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X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going from protein to structure. In practice, the crystallization process proceeds through knowledge-informed empiricism. Better physico-chemical understanding remains elusive because of the large number of variables involved, hence little guidance is available to systematically identify solution conditions that promote crystallization. To help determine relationships between macromolecular properties and their crystallization propensity, we have trained statistical models on samples for 182 proteins supplied by the Northeast Structural Genomics consortium. Gaussian processes, which capture trends beyond the reach of linear statistical models, distinguish between two main physico-chemical mechanisms driving crystallization. One is characterized by low levels of side chain entropy and has been extensively reported in the literature. The other identifies specific electrostatic interactions not previously described in the crystallization context. Because evidence for two distinct mechanisms can be gleaned both from crystal contacts and from solution conditions leading to successful crystallization, the model offers future avenues for optimizing crystallization screens based on partial structural information. The availability of crystallization data coupled with structural outcomes analyzed through state-of-the-art statistical models may thus guide macromolecular crystallization toward a more rational basis.

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On the need for an international effort to capture, share and use crystallization screening data

Abstract: Development of an ontology for the description of crystallization experiments and results is proposed.

Cited by 39 publications

References 32 publications

Soft matter perspective on protein crystal assembly

Soft matter perspective on protein crystal assembly

An Overview of Biological Macromolecule Crystallization

Statistical Analysis of Crystallization Database Links Protein Physico-Chemical Features with Crystallization Mechanisms

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