Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

Wolff, Alexander M.; Young, Iris D.; Sierra, Raymond G.; Brewster, Aaron S.; Martynowycz, Michael W.; Nango, Eriko; Sugahara, Michihiro; Nakane, Takanori; Ito, Kazutaka; Aquila, Andrew; Bhowmick, Asmit; Biel, Justin T.; Carbajo, Sergio; Cohen, Aina E.; Cortez, Saul; Gonzalez, Ana; Hino, Tomoya; Im, Dohyun; Koralek, Jake D.; Kubo, Minoru; Lazarou, Tomas S.; Nomura, Takashi; Owada, Shigeki; Samelson, Avi J.; Tanaka, Tomoyuki; Tanaka, Rie; Thompson, Erin M.; van den Bedem, Henry; Woldeyes, Rahel A.; Yumoto, Fumiaki; Zhao, Wei; Tono, Kensuke; Boutet, Sebastien; Iwata, So; Gonen, Tamir; Sauter, Nicholas K.; Fraser, James S.; Thompson, Michael C.

doi:10.1107/S205225252000072X

Title: Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

Journal Article · Wed Feb 26 00:00:00 EST 2020 · IUCrJ

DOI:https://doi.org/10.1107/S205225252000072X· OSTI ID:1617957

; Young, Iris D.; Sierra, Raymond G.; Brewster, Aaron S.; Martynowycz, Michael W.;

; Sugahara, Michihiro;

; Ito, Kazutaka; Aquila, Andrew; Bhowmick, Asmit; Biel, Justin T.;

;

; Gonzalez, Ana; Hino, Tomoya; Im, Dohyun; Koralek, Jake D.; Kubo, Minoru more »

Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme.

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Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division; National Science Foundation (NSF); National Institutes of Health (NIH)

Grant/Contract Number:: AC02-05CH11231; AC02-76SF00515; STC-1231306; F32 HL129989; GM123159; GM124149; GM117126; LFR-17-476732

OSTI ID:: 1617957

Alternate ID(s):: OSTI ID: 1615313; OSTI ID: 1617040

Journal Information:: IUCrJ, Journal Name: IUCrJ Vol. 7 Journal Issue: 2; ISSN 2052-2525

Publisher:: International Union of CrystallographyCopyright Statement

Country of Publication:: United Kingdom

Language:: English

Citation Metrics:

Cited by: 15 works

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References (62)

Hidden alternative structures of proline isomerase essential for catalysis Fraser, James S.; Clarkson, Michael W.; Degnan, Sheena C. Nature, Vol. 462, Issue 7273 https://doi.org/10.1038/nature08615	journal	December 2009
Biomolecular cryocrystallography: Structural changes during flash-cooling Halle, B. Proceedings of the National Academy of Sciences, Vol. 101, Issue 14 https://doi.org/10.1073/pnas.0308315101	journal	March 2004
Cheetah : software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data Barty, Anton; Kirian, Richard A.; Maia, Filipe R. N. C. Journal of Applied Crystallography, Vol. 47, Issue 3 https://doi.org/10.1107/S1600576714007626	journal	May 2014
Electron diffraction and three-dimensional crystallography for structural biology Clabbers, Max T. B.; Abrahams, Jan Pieter Crystallography Reviews, Vol. 24, Issue 3 https://doi.org/10.1080/0889311X.2018.1446427	journal	January 2018
Development of an X-ray pixel detector with multi-port charge-coupled device for X-ray free-electron laser experiments Kameshima, Takashi; Ono, Shun; Kudo, Togo Review of Scientific Instruments, Vol. 85, Issue 3 https://doi.org/10.1063/1.4867668	journal	March 2014
Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography Mueller, C.; Marx, A.; Epp, S. W. Structural Dynamics, Vol. 2, Issue 5 https://doi.org/10.1063/1.4928706	journal	August 2015
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
Grease matrix as a versatile carrier of proteins for serial crystallography Sugahara, Michihiro; Mizohata, Eiichi; Nango, Eriko Nature Methods, Vol. 12, Issue 1 https://doi.org/10.1038/nmeth.3172	journal	November 2014
MeshAndCollect : an automated multi-crystal data-collection workflow for synchrotron macromolecular crystallography beamlines Zander, Ulrich; Bourenkov, Gleb; Popov, Alexander N. Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 11 https://doi.org/10.1107/S1399004715017927	journal	October 2015
Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED de la Cruz, M. Jason; Hattne, Johan; Shi, Dan Nature Methods, Vol. 14, Issue 4 https://doi.org/10.1038/nmeth.4178	journal	February 2017
DIALS : implementation and evaluation of a new integration package Winter, Graeme; Waterman, David G.; Parkhurst, James M. Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 2 https://doi.org/10.1107/S2059798317017235	journal	February 2018
ImageJ2: ImageJ for the next generation of scientific image data Rueden, Curtis T.; Schindelin, Johannes; Hiner, Mark C. BMC Bioinformatics, Vol. 18, Issue 1 https://doi.org/10.1186/s12859-017-1934-z	journal	November 2017
Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation Martin-Garcia, Jose M.; Conrad, Chelsie E.; Nelson, Garrett IUCrJ, Vol. 4, Issue 4, p. 439-454 https://doi.org/10.1107/S205225251700570X	journal	May 2017
Femtosecond X-ray protein nanocrystallography Chapman, Henry N.; Fromme, Petra; Barty, Anton Nature, Vol. 470, Issue 7332, p. 73-77 https://doi.org/10.1038/nature09750	journal	February 2011
Electric-field-stimulated protein mechanics Hekstra, Doeke R.; White, K. Ian; Socolich, Michael A. Nature, Vol. 540, Issue 7633 https://doi.org/10.1038/nature20571	journal	December 2016
Towards automated crystallographic structure refinement with phenix.refine Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4 https://doi.org/10.1107/S0907444912001308	journal	March 2012
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10 https://doi.org/10.1107/S2059798319011471	journal	October 2019
Intrinsic dynamics of an enzyme underlies catalysis Eisenmesser, Elan Z.; Millet, Oscar; Labeikovsky, Wladimir Nature, Vol. 438, Issue 7064 https://doi.org/10.1038/nature04105	journal	November 2005
Electron diffraction data processing with DIALS Clabbers, Max T. B.; Gruene, Tim; Parkhurst, James M. Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 6 https://doi.org/10.1107/S2059798318007726	journal	May 2018
Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers Fuller, Franklin D.; Gul, Sheraz; Chatterjee, Ruchira Nature Methods, Vol. 14, Issue 4 https://doi.org/10.1038/nmeth.4195	journal	February 2017
Diverse application platform for hard X-ray diffraction in SACLA (DAPHNIS): application to serial protein crystallography using an X-ray free-electron laser Tono, Kensuke; Nango, Eriko; Sugahara, Michihiro Journal of Synchrotron Radiation, Vol. 22, Issue 3 https://doi.org/10.1107/S1600577515004464	journal	April 2015
Diverse HIV viruses are targeted by a conformationally dynamic antiviral Caines, Matthew E. C.; Bichel, Katsiaryna; Price, Amanda J. Nature Structural & Molecular Biology, Vol. 19, Issue 4 https://doi.org/10.1038/nsmb.2253	journal	March 2012
Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography Coquelle, Nicolas; Sliwa, Michel; Woodhouse, Joyce Nature Chemistry, Vol. 10, Issue 1 https://doi.org/10.1038/nchem.2853	journal	September 2017
Modelling dynamics in protein crystal structures by ensemble refinement Burnley, B. Tom; Afonine, Pavel V.; Adams, Paul D. eLife, Vol. 1 https://doi.org/10.7554/eLife.00311	journal	December 2012
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
Indexing in single-crystal diffractometry with an obstinate list of reflections Duisenberg, A. J. M. Journal of Applied Crystallography, Vol. 25, Issue 2 https://doi.org/10.1107/S0021889891010634	journal	April 1992
X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex Zhou, X. Edward; Gao, Xiang; Barty, Anton Scientific Data, Vol. 3, Issue 1 https://doi.org/10.1038/sdata.2016.21	journal	April 2016
Serial Femtosecond Crystallography of G Protein-Coupled Receptors Liu, W.; Wacker, D.; Gati, C. Science, Vol. 342, Issue 6165 https://doi.org/10.1126/science.1244142	journal	December 2013
Recent developments in CrystFEL White, Thomas A.; Mariani, Valerio; Brehm, Wolfgang Journal of Applied Crystallography, Vol. 49, Issue 2 https://doi.org/10.1107/S1600576716004751	journal	March 2016
Hydroxyethyl cellulose matrix applied to serial crystallography Sugahara, Michihiro; Nakane, Takanori; Masuda, Tetsuya Scientific Reports, Vol. 7, Article No. 703 https://doi.org/10.1038/s41598-017-00761-0	journal	April 2017
Data processing pipeline for serial femtosecond crystallography at SACLA Nakane, Takanori; Joti, Yasumasa; Tono, Kensuke Journal of Applied Crystallography, Vol. 49, Issue 3 https://doi.org/10.1107/S1600576716005720	journal	April 2016
Structure of photosystem II and substrate binding at room temperature Young, Iris D.; Ibrahim, Mohamed; Chatterjee, Ruchira Nature, Vol. 540, Issue 7633 https://doi.org/10.1038/nature20161	journal	November 2016
A compact X-ray free-electron laser emitting in the sub-ångström region Ishikawa, Tetsuya; Aoyagi, Hideki; Asaka, Takao Nature Photonics, Vol. 6, Issue 8 https://doi.org/10.1038/nphoton.2012.141	journal	June 2012
The Macromolecular Femtosecond Crystallography Instrument at the Linac Coherent Light Source Sierra, Raymond G.; Batyuk, Alexander; Sun, Zhibin Journal of Synchrotron Radiation, Vol. 26, Issue 2 https://doi.org/10.1107/S1600577519001577	journal	February 2019
Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography Keedy, Daniel A.; Kenner, Lillian R.; Warkentin, Matthew eLife, Vol. 4 https://doi.org/10.7554/eLife.07574	journal	September 2015
Small is beautiful: protein micro-crystallography Cusack, Stephen; Belrhali, Hassan; Bram, Andreas Nature Structural Biology, Vol. 5, Issue 8 https://doi.org/10.1038/1325	journal	August 1998
Collection of Continuous Rotation MicroED Data from Ion Beam-Milled Crystals of Any Size Martynowycz, Michael W.; Zhao, Wei; Hattne, Johan Structure, Vol. 27, Issue 3 https://doi.org/10.1016/j.str.2018.12.003	journal	March 2019
Structure of the toxic core of α-synuclein from invisible crystals Rodriguez, Jose A.; Ivanova, Magdalena I.; Sawaya, Michael R. Nature, Vol. 525, Issue 7570 https://doi.org/10.1038/nature15368	journal	September 2015
Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography Weierstall, Uwe; James, Daniel; Wang, Chong Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms4309	journal	February 2014
Multiple-beamline operation of SACLA Tono, Kensuke; Hara, Toru; Yabashi, Makina Journal of Synchrotron Radiation, Vol. 26, Issue 2 https://doi.org/10.1107/S1600577519001607	journal	February 2019
Fixed-target protein serial microcrystallography with an x-ray free electron laser Hunter, Mark S.; Segelke, Brent; Messerschmidt, Marc Scientific Reports, Vol. 4, Issue 1 https://doi.org/10.1038/srep06026	journal	August 2014
Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II Sierra, Raymond G.; Gati, Cornelius; Laksmono, Hartawan Nature Methods, Vol. 13, Issue 1 https://doi.org/10.1038/nmeth.3667	journal	November 2015
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Modeling truncated pixel values of faint reflections in MicroED images Hattne, Johan; Shi, Dan; de la Cruz, M. Jason Journal of Applied Crystallography, Vol. 49, Issue 3 https://doi.org/10.1107/S1600576716007196	journal	May 2016
REFMAC 5 for the refinement of macromolecular crystal structures Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911001314	journal	March 2011
Estimates of internal stress and related mosaicity in solution grown crystals: proteins Chernov, A. A. Journal of Crystal Growth, Vol. 196, Issue 2-4 https://doi.org/10.1016/S0022-0248(98)00836-7	journal	January 1999
High-density grids for efficient data collection from multiple crystals Baxter, Elizabeth L.; Aguila, Laura; Alonso-Mori, Roberto Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 1, p. 2-11 https://doi.org/10.1107/S2059798315020847	journal	January 2016
Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL Suga, Michihiro; Akita, Fusamichi; Sugahara, Michihiro Nature, Vol. 543, Issue 7643 https://doi.org/10.1038/nature21400	journal	February 2017
Machining protein microcrystals for structure determination by electron diffraction Duyvesteyn, Helen M. E.; Kotecha, Abhay; Ginn, Helen M. Proceedings of the National Academy of Sciences, Vol. 115, Issue 38 https://doi.org/10.1073/pnas.1809978115	journal	August 2018
Improving signal strength in serial crystallography with DIALS geometry refinement Brewster, Aaron S.; Waterman, David G.; Parkhurst, James M. Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 9 https://doi.org/10.1107/S2059798318009191	journal	September 2018
An introduction to data reduction: space-group determination, scaling and intensity statistics Evans, Philip R. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S090744491003982X	journal	March 2011
XFEL diffraction: developing processing methods to optimize data quality Sauter, Nicholas K. Journal of Synchrotron Radiation, Vol. 22, Issue 2 https://doi.org/10.1107/S1600577514028203	journal	January 2015
High-resolution structure determination by continuous-rotation data collection in MicroED Nannenga, Brent L.; Shi, Dan; Leslie, Andrew G. W. Nature Methods, Vol. 11, Issue 9 https://doi.org/10.1038/nmeth.3043	journal	August 2014
The complementarity of serial femtosecond crystallography and MicroED for structure determination from microcrystals Zatsepin, Nadia A.; Li, Chufeng; Colasurd, Paige Current Opinion in Structural Biology, Vol. 58 https://doi.org/10.1016/j.sbi.2019.06.004	journal	October 2019
Improvements in serial femtosecond crystallography of photosystem II by optimizing crystal uniformity using microseeding procedures Ibrahim, Mohamed; Chatterjee, Ruchira; Hellmich, Julia Structural Dynamics, Vol. 2, Issue 4 https://doi.org/10.1063/1.4919741	journal	July 2015
A three-dimensional movie of structural changes in bacteriorhodopsin Nango, Eriko; Royant, Antoine; Kubo, Minoru Science, Vol. 354, Issue 6319, p. 1552-1557 https://doi.org/10.1126/science.aah3497	journal	December 2016
Qualitative Analyses of Polishing and Precoating FIB Milled Crystals for MicroED Martynowycz, Michael W.; Zhao, Wei; Hattne, Johan Structure, Vol. 27, Issue 10 https://doi.org/10.1016/j.str.2019.07.004	journal	October 2019
Real-Time Observation of Protein Dense Liquid Cluster Evolution during Nucleation in Protein Crystallization Schubert, Robin; Meyer, Arne; Baitan, Daniela Crystal Growth & Design, Vol. 17, Issue 3 https://doi.org/10.1021/acs.cgd.6b01826	journal	January 2017
Three-dimensional electron crystallography of protein microcrystals Shi, Dan; Nannenga, Brent L.; Iadanza, Matthew G. eLife, Vol. 2 https://doi.org/10.7554/eLife.01345	journal	November 2013
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
The cryo-EM method microcrystal electron diffraction (MicroED) Nannenga, Brent L.; Gonen, Tamir Nature Methods, Vol. 16, Issue 5 https://doi.org/10.1038/s41592-019-0395-x	journal	April 2019
Nanoflow electrospinning serial femtosecond crystallography Sierra, Raymond G.; Laksmono, Hartawan; Kern, Jan Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 11, p. 1584-1587 https://doi.org/10.1107/S0907444912038152	journal	October 2012

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Title: Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

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