Literature DB >> 21643490

What's in a drop? Correlating observations and outcomes to guide macromolecular crystallization experiments.

Joseph R Luft1, Jennifer R Wolfley, Edward H Snell.   

Abstract

Observations of crystallization experiments are classified as specific outcomes and integrated through a phase diagram to visualize solubility and thereby direct subsequent experiments. Specific examples are taken from our high-throughput crystallization laboratory which provided a broad scope of data from 20 million crystallization experiments on 12,500 different biological macromolecules. The methods and rationale are broadly and generally applicable in any crystallization laboratory. Through a combination of incomplete factorial sampling of crystallization cocktails, standard outcome classifications, visualization of outcomes as they relate chemically and application of a simple phase diagram approach we demonstrate how to logically design subsequent crystallization experiments.

Entities:  

Year:  2011        PMID: 21643490      PMCID: PMC3106348          DOI: 10.1021/cg1013945

Source DB:  PubMed          Journal:  Cryst Growth Des        ISSN: 1528-7483            Impact factor:   4.076


  43 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid.

Authors:  J D WATSON; F H CRICK
Journal:  Nature       Date:  1953-04-25       Impact factor: 49.962

3.  Effects of pH on protein-protein interactions and implications for protein phase behavior.

Authors:  André C Dumetz; Aaron M Chockla; Eric W Kaler; Abraham M Lenhoff
Journal:  Biochim Biophys Acta       Date:  2008-01-16

4.  Patterns of protein protein interactions in salt solutions and implications for protein crystallization.

Authors:  André C Dumetz; Ann M Snellinger-O'brien; Eric W Kaler; Abraham M Lenhoff
Journal:  Protein Sci       Date:  2007-09       Impact factor: 6.725

5.  AutoSherlock: a program for effective crystallization data analysis.

Authors:  Raymond M Nagel; Joseph R Luft; Edward H Snell
Journal:  J Appl Crystallogr       Date:  2008-10-11       Impact factor: 3.304

6.  Protein crystallization analysis on the World Community Grid.

Authors:  Christian A Cumbaa; Igor Jurisica
Journal:  J Struct Funct Genomics       Date:  2010-01-14

7.  Shotgun crystallization strategy for structural genomics: an optimized two-tiered crystallization screen against the Thermotoga maritima proteome.

Authors:  Rebecca Page; Slawomir K Grzechnik; Jaume M Canaves; Glen Spraggon; Andreas Kreusch; Peter Kuhn; Raymond C Stevens; Scott A Lesley
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2003-05-23

8.  X-ray structure analysis of a membrane protein complex. Electron density map at 3 A resolution and a model of the chromophores of the photosynthetic reaction center from Rhodopseudomonas viridis.

Authors:  J Deisenhofer; O Epp; K Miki; R Huber; H Michel
Journal:  J Mol Biol       Date:  1984-12-05       Impact factor: 5.469

9.  The application and use of chemical space mapping to interpret crystallization screening results.

Authors:  Edward H Snell; Ray M Nagel; Ann Wojtaszcyk; Hugh O'Neill; Jennifer L Wolfley; Joseph R Luft
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2008-11-18

10.  Establishing a training set through the visual analysis of crystallization trials. Part I: approximately 150,000 images.

Authors:  Edward H Snell; Joseph R Luft; Stephen A Potter; Angela M Lauricella; Stacey M Gulde; Michael G Malkowski; Mary Koszelak-Rosenblum; Meriem I Said; Jennifer L Smith; Christina K Veatch; Robert J Collins; Geoff Franks; Max Thayer; Christian Cumbaa; Igor Jurisica; George T Detitta
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2008-10-18
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  19 in total

1.  The use of haptic interfaces and web services in crystallography: an application for a 'screen to beam' interface.

Authors:  Andrew E Bruno; Alexei S Soares; Robin L Owen; Edward H Snell
Journal:  J Appl Crystallogr       Date:  2016-11-11       Impact factor: 3.304

2.  Cinder: keeping crystallographers app-y.

Authors:  Nicholas Rosa; Marko Ristic; Bevan Marshall; Janet Newman
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2018-06-26       Impact factor: 1.056

3.  Towards protein-crystal centering using second-harmonic generation (SHG) microscopy.

Authors:  David J Kissick; Christopher M Dettmar; Michael Becker; Anne M Mulichak; Vadim Cherezov; Stephan L Ginell; Kevin P Battaile; Lisa J Keefe; Robert F Fischetti; Garth J Simpson
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2013-04-19

4.  Minimal physical requirements for crystal growth self-poisoning.

Authors:  Stephen Whitelam; Yuba Raj Dahal; Jeremy D Schmit
Journal:  J Chem Phys       Date:  2016-02-14       Impact factor: 3.488

5.  Water in the formation of biogenic minerals: peeling away the hydration layers.

Authors:  Jason R Dorvee; Arthur Veis
Journal:  J Struct Biol       Date:  2013-06-19       Impact factor: 2.867

6.  Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization.

Authors:  R Lasala; N Coudray; A Abdine; Z Zhang; M Lopez-Redondo; R Kirshenbaum; J Alexopoulos; Z Zolnai; D L Stokes; I Ubarretxena-Belandia
Journal:  J Struct Biol       Date:  2014-12-03       Impact factor: 2.867

Review 7.  Computational crystallization.

Authors:  Irem Altan; Patrick Charbonneau; Edward H Snell
Journal:  Arch Biochem Biophys       Date:  2016-01-11       Impact factor: 4.013

Review 8.  MicroED in natural product and small molecule research.

Authors:  Emma Danelius; Steve Halaby; Wilfred A van der Donk; Tamir Gonen
Journal:  Nat Prod Rep       Date:  2020-09-17       Impact factor: 13.423

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

Authors:  Janet Newman; Evan E Bolton; Jochen Müller-Dieckmann; Vincent J Fazio; D Travis Gallagher; David Lovell; Joseph R Luft; Thomas S Peat; David Ratcliffe; Roger A Sayle; Edward H Snell; Kerry Taylor; Pascal Vallotton; Sameer Velanker; Frank von Delft
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2012-02-15

10.  Using isoelectric point to determine the pH for initial protein crystallization trials.

Authors:  Jobie Kirkwood; David Hargreaves; Simon O'Keefe; Julie Wilson
Journal:  Bioinformatics       Date:  2015-01-07       Impact factor: 6.937

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