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Title: Sample manipulation and data assembly for robust microcrystal synchrotron crystallography

Abstract

With the recent developments in microcrystal handling, synchrotron microdiffraction beamline instrumentation and data analysis, microcrystal crystallography with crystal sizes of less than 10 µm is appealing at synchrotrons. However, challenges remain in sample manipulation and data assembly for robust microcrystal synchrotron crystallography. Here, the development of micro-sized polyimide well-mounts for the manipulation of microcrystals of a few micrometres in size and the implementation of a robust data-analysis method for the assembly of rotational microdiffraction data sets from many microcrystals are described. The method demonstrates that microcrystals may be routinely utilized for the acquisition and assembly of complete data sets from synchrotron microdiffraction beamlines.

Authors:
; ORCiD logo; ; ; ORCiD logo; ; ; ; ORCiD logo
Publication Date:
Research Org.:
Brookhaven National Lab. (BNL), Upton, NY (United States); Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); National Institutes of Health (NIH)
OSTI Identifier:
1433744
Alternate Identifier(s):
OSTI ID: 1434774; OSTI ID: 1466304
Report Number(s):
BNL-203558-2018-JAAM
Journal ID: ISSN 2052-2525; IUCRAJ; PII: S2052252518005389
Grant/Contract Number:  
SC0012704; KC0401040; AC02-06CH11357
Resource Type:
Published Article
Journal Name:
IUCrJ
Additional Journal Information:
Journal Name: IUCrJ Journal Volume: 5 Journal Issue: 3; Journal ID: ISSN 2052-2525
Publisher:
International Union of Crystallography
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; microcrystals; microdiffraction; radiation damage; data analysis; multiple crystals; X-ray crystallography; structural biology; microcrystal

Citation Formats

Guo, Gongrui, Fuchs, Martin R., Shi, Wuxian, Skinner, John, Berman, Evanna, Ogata, Craig M., Hendrickson, Wayne A., McSweeney, Sean, and Liu, Qun. Sample manipulation and data assembly for robust microcrystal synchrotron crystallography. United Kingdom: N. p., 2018. Web. doi:10.1107/S2052252518005389.
Guo, Gongrui, Fuchs, Martin R., Shi, Wuxian, Skinner, John, Berman, Evanna, Ogata, Craig M., Hendrickson, Wayne A., McSweeney, Sean, & Liu, Qun. Sample manipulation and data assembly for robust microcrystal synchrotron crystallography. United Kingdom. doi:10.1107/S2052252518005389.
Guo, Gongrui, Fuchs, Martin R., Shi, Wuxian, Skinner, John, Berman, Evanna, Ogata, Craig M., Hendrickson, Wayne A., McSweeney, Sean, and Liu, Qun. Thu . "Sample manipulation and data assembly for robust microcrystal synchrotron crystallography". United Kingdom. doi:10.1107/S2052252518005389.
@article{osti_1433744,
title = {Sample manipulation and data assembly for robust microcrystal synchrotron crystallography},
author = {Guo, Gongrui and Fuchs, Martin R. and Shi, Wuxian and Skinner, John and Berman, Evanna and Ogata, Craig M. and Hendrickson, Wayne A. and McSweeney, Sean and Liu, Qun},
abstractNote = {With the recent developments in microcrystal handling, synchrotron microdiffraction beamline instrumentation and data analysis, microcrystal crystallography with crystal sizes of less than 10 µm is appealing at synchrotrons. However, challenges remain in sample manipulation and data assembly for robust microcrystal synchrotron crystallography. Here, the development of micro-sized polyimide well-mounts for the manipulation of microcrystals of a few micrometres in size and the implementation of a robust data-analysis method for the assembly of rotational microdiffraction data sets from many microcrystals are described. The method demonstrates that microcrystals may be routinely utilized for the acquisition and assembly of complete data sets from synchrotron microdiffraction beamlines.},
doi = {10.1107/S2052252518005389},
journal = {IUCrJ},
number = 3,
volume = 5,
place = {United Kingdom},
year = {2018},
month = {4}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1107/S2052252518005389

Citation Metrics:
Cited by: 5 works
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Works referenced in this record:

Single mimivirus particles intercepted and imaged with an X-ray laser
journal, February 2011

  • Seibert, M. Marvin; Ekeberg, Tomas; Maia, Filipe R. N. C.
  • Nature, Vol. 470, Issue 7332
  • DOI: 10.1038/nature09748

Structures from Anomalous Diffraction of Native Biological Macromolecules
journal, May 2012


Micro-crystallography comes of age
journal, October 2012

  • Smith, Janet L.; Fischetti, Robert F.; Yamamoto, Masaki
  • Current Opinion in Structural Biology, Vol. 22, Issue 5
  • DOI: 10.1016/j.sbi.2012.09.001

Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography
journal, August 2015

  • Mueller, C.; Marx, A.; Epp, S. W.
  • Structural Dynamics, Vol. 2, Issue 5
  • DOI: 10.1063/1.4928706

Serial crystallography on in vivo grown microcrystals using synchrotron radiation
journal, February 2014


Overview of the CCP 4 suite and current developments
journal, March 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910045749

MeshAndCollect : an automated multi-crystal data-collection workflow for synchrotron macromolecular crystallography beamlines
journal, October 2015

  • Zander, Ulrich; Bourenkov, Gleb; Popov, Alexander N.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 11
  • DOI: 10.1107/S1399004715017927

Room-temperature macromolecular serial crystallography using synchrotron radiation
journal, May 2014


Robust structural analysis of native biological macromolecules from multi-crystal anomalous diffraction data
journal, June 2013

  • Liu, Qun; Liu, Qinglian; Hendrickson, Wayne A.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7
  • DOI: 10.1107/S0907444913001479

DIALS : implementation and evaluation of a new integration package
journal, February 2018

  • Winter, Graeme; Waterman, David G.; Parkhurst, James M.
  • Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 2
  • DOI: 10.1107/S2059798317017235

High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography
journal, May 2012


Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation
journal, May 2017

  • Martin-Garcia, Jose M.; Conrad, Chelsie E.; Nelson, Garrett
  • IUCrJ, Vol. 4, Issue 4, p. 439-454
  • DOI: 10.1107/S205225251700570X

Femtosecond X-ray protein nanocrystallography
journal, February 2011

  • Chapman, Henry N.; Fromme, Petra; Barty, Anton
  • Nature, Vol. 470, Issue 7332, p. 73-77
  • DOI: 10.1038/nature09750

Towards automated crystallographic structure refinement with phenix.refine
journal, March 2012

  • Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel
  • Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4
  • DOI: 10.1107/S0907444912001308

PROCHECK: a program to check the stereochemical quality of protein structures
journal, April 1993

  • Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.
  • Journal of Applied Crystallography, Vol. 26, Issue 2
  • DOI: 10.1107/S0021889892009944

Mix-and-diffuse serial synchrotron crystallography
journal, October 2017


Predicting the X-ray lifetime of protein crystals
journal, December 2013

  • Zeldin, O. B.; Brockhauser, S.; Bremridge, J.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 51
  • DOI: 10.1073/pnas.1315879110

How good are my data and what is the resolution?
journal, June 2013

  • Evans, Philip R.; Murshudov, Garib N.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7
  • DOI: 10.1107/S0907444913000061

Serial femtosecond crystallography: the first five years
journal, February 2015


NSLS-II biomedical beamlines for micro-crystallography, FMX, and for highly automated crystallography, AMX: New opportunities for advanced data collection
conference, January 2016

  • Fuchs, Martin R.; Bhogadi, Dileep K.; Jakoncic, Jean
  • PROCEEDINGS OF THE 12TH INTERNATIONAL CONFERENCE ON SYNCHROTRON RADIATION INSTRUMENTATION – SRI2015, AIP Conference Proceedings
  • DOI: 10.1063/1.4952829

Glass transition in thaumatin crystals revealed through temperature-dependent radiation-sensitivity measurements
journal, September 2010

  • Warkentin, Matthew; Thorne, Robert E.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 10
  • DOI: 10.1107/S0907444910035523

Improved reproducibility of unit-cell parameters in macromolecular cryocrystallography by limiting dehydration during crystal mounting
journal, July 2014

  • Farley, Christopher; Burks, Geoffry; Siegert, Thomas
  • Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 8
  • DOI: 10.1107/S1399004714012310

The application of hierarchical cluster analysis to the selection of isomorphous crystals
journal, May 2012

  • Giordano, Rita; Leal, Ricardo M. F.; Bourenkov, Gleb P.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 6
  • DOI: 10.1107/S0907444912006841

Efficient merging of data from multiple samples for determination of anomalous substructure
journal, March 2016

  • Akey, David L.; Terwilliger, Thomas C.; Smith, Janet L.
  • Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 3
  • DOI: 10.1107/S2059798315021920

Automated identification of elemental ions in macromolecular crystal structures
journal, March 2014

  • Echols, Nathaniel; Morshed, Nader; Afonine, Pavel V.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 4
  • DOI: 10.1107/S1399004714001308

Diffraction-geometry refinement in the DIALS framework
journal, March 2016

  • Waterman, David G.; Winter, Graeme; Gildea, Richard J.
  • Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 4
  • DOI: 10.1107/S2059798316002187

Macromolecular microcrystallography
journal, April 2011


Room-temperature serial crystallography at synchrotron X-ray sources using slowly flowing free-standing high-viscosity microstreams
journal, January 2015

  • Botha, Sabine; Nass, Karol; Barends, Thomas R. M.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 2
  • DOI: 10.1107/S1399004714026327

Processing and post-refinement of oscillation camera data
journal, December 1979

  • Rossmann, M. G.; Leslie, A. G. W.; Abdel-Meguid, S. S.
  • Journal of Applied Crystallography, Vol. 12, Issue 6
  • DOI: 10.1107/S0021889879013273

Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography
journal, July 2013

  • Foadi, James; Aller, Pierre; Alguel, Yilmaz
  • Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 8
  • DOI: 10.1107/S0907444913012274

EIGER detector: application in macromolecular crystallography
journal, August 2016

  • Casanas, Arnau; Warshamanage, Rangana; Finke, Aaron D.
  • Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 9
  • DOI: 10.1107/S2059798316012304

MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009

  • Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
  • DOI: 10.1107/S0907444909042073

Fully automatic macromolecular crystallography: the impact of MASSIF-1 on the optimum acquisition and quality of data
journal, March 2016


Features and development of Coot
journal, March 2010

  • Emsley, P.; Lohkamp, B.; Scott, W. G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007493

Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal
journal, March 2016

  • Terwilliger, Thomas C.; Bunkóczi, Gábor; Hung, Li-Wei
  • Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 3
  • DOI: 10.1107/S2059798315019403

Multi-crystal native SAD analysis at 6 keV
journal, September 2014

  • Liu, Qun; Guo, Youzhong; Chang, Yanqi
  • Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 10
  • DOI: 10.1107/S1399004714013376

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams
journal, April 2015

  • Coquelle, Nicolas; Brewster, Aaron S.; Kapp, Ulrike
  • Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 5
  • DOI: 10.1107/S1399004715004514

Room-temperature macromolecular crystallography using a micro-patterned silicon chip with minimal background scattering
journal, May 2016

  • Roedig, Philip; Duman, Ramona; Sanchez-Weatherby, Juan
  • Journal of Applied Crystallography, Vol. 49, Issue 3
  • DOI: 10.1107/S1600576716006348

Lipidic cubic phase serial millisecond crystallography using synchrotron radiation
journal, March 2015


Pink-beam serial crystallography
journal, November 2017


A micro-patterned silicon chip as sample holder for macromolecular crystallography experiments with minimal background scattering
journal, May 2015

  • Roedig, P.; Vartiainen, I.; Duman, R.
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep10451

Experimental phasing with SHELXC / D / E : combining chain tracing with density modification
journal, March 2010

  • Sheldrick, George M.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444909038360

Experimental determination of the radiation dose limit for cryocooled protein crystals
journal, March 2006

  • Owen, R. L.; Rudino-Pinera, E.; Garman, E. F.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 13
  • DOI: 10.1073/pnas.0600973103

Protein microcrystallography using synchrotron radiation
journal, August 2017


Merging of synchrotron serial crystallographic data by a genetic algorithm
journal, August 2016

  • Zander, Ulrich; Cianci, Michele; Foos, Nicolas
  • Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 9
  • DOI: 10.1107/S2059798316012079

Crystal Structure of a Lipid G Protein-Coupled Receptor
journal, February 2012


The minimum crystal size needed for a complete diffraction data set
journal, March 2010

  • Holton, James M.; Frankel, Kenneth A.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007262

XFELs for structure and dynamics in biology
journal, May 2017


How baculovirus polyhedra fit square pegs into round holes to robustly package viruses
journal, December 2009


A multicrystal diffraction data-collection approach for studying structural dynamics with millisecond temporal resolution
journal, October 2016


    Works referencing / citing this record:

    Synchrotron microcrystal native-SAD phasing at a low energy
    journal, May 2019


    Sulfur-SAD phasing from microcrystals utilizing low-energy X-rays
    journal, June 2019


    Synchrotron microcrystal native-SAD phasing at a low energy
    journal, May 2019


    Sulfur-SAD phasing from microcrystals utilizing low-energy X-rays
    journal, June 2019