Crystallization

X-ray crystallography is the method of choice for solving the structure of molecules with the size up to 1 MDa, while most typical systems consist of ordered domain structures from few 100 kDa to peptides and small molecules. Crystallography is the most popular structural biology method in use. The main requirement is that your sample is ordered and pure enough to crystallize. Macromolecular crystallisation requires few milligran amounts of purified protein, and can yield higher resolution structures  than any other technique.

Robots are key to the expansion of macromolecular crystallography. They can accurately handle nanolitre volumes and so do the crystallisation experiments with only 5-10% of the protein required for manual setup. The small drops also equilibrate faster allowing faster analysis of the results.

For each 96-formatted screen, we ask you to provide 20 ul of the concentrated protein sample. We prepare the sample for the crystallisation, dispense all crystallisation solutions and the protein drops on the crystallisation plate, seal plates and image the experiment. You will get an access to the a viewer program (PiXray)  to look at the images and the history of each drop.

The X-ray unit offers standard and optimized crystallization services, including lipid phase crystallization of membrane proteins. The X-ray unit also jointly organizes the shipment of crystals and the data collection at synchrotrons by coordinated Block-Allocation-Group (BAG)-proposals, ESRF and MAXLAB-IV (Kajander, Helsinki) and at Diamond (Lehtiö, Oulu) on the national level of Instruct-FI.  New in situ crystallization screening will also be implemented to facilitate rapid evaluation of crystal diffraction in 2018.

Current crystallography services include (see also additional services below):

  • Advice on protein production and purification for structural studies.
  • Standard set of crystallization screens for crystallization at +4 and RT
  • Imaging of plates and access to viewing the results online
  • Optimisation of the crystallization hits
  • Preparation of crystallisation stock solutions
  • Analysis of crystals for diffraction at synchtrons (or in-house, end of 2018 onwards)
  • Structure determination and analysis (collaboration)

Robots are key to the expansion of macromolecular crystallography. They can accurately handle nanolitre volumes and so do the crystallisation experiments with only 5-10% of the protein required for manual setup. The small drops also equilibrate faster allowing faster analysis of the results.

For each 96-formatted screen, we ask you to provide 20 ul of the concentrated protein sample. We prepare the sample for the crystallisation, dispense all crystallisation solutions and the protein drops on the crystallisation plate, seal plates and image the experiment. You will get an access to the program PiXray  to look at the images and the history of each drop. A more detailed description of our services can be found here (link).

Additional services

  • Screening of protein stability prior to crystallisation and optimisation with fluorescence-based thermal shift assay (Thermofluor) (Equipment: Stratagene Mx 3005P).
  • Analytical SEC-MALLS (analytical size exclusion chromatography couped with light scattering to determine size distribution, monodispersity and oligomeric state and protein conjugate complex composition (e.g. glycoproteins, membrane proteins, PEGylated samples, protein-DNA compexes)
  • Screening of the temperature dependence of three-dimensional crystal formation of protein, using Eppendorf Mastercycler gradient thermocycler (Thermo-screening).
  • Help with protein expression and purification and sample polishing (mainly collaboration).
  • Overall highest resolution method for structural studies of macromolecus (only method for atomic resolution information currenly; to higher than >1.5 Å resolution)
  • Structual studies of protein-protein complexes, enzyme mechanism, screening and inhibitor complex studies
  • Structural studies of membrane proteins
  • Pre-screening for stability and homogeneity and monodispersity of samples, inhibitor binding studies
  • Determination of oligomeric state of complexes and composition of protein conjugate complexes (e.g. membrane protein detergent complex, proteoglycans etc)

Protein crystallisation platform has multiple robotic devices:

  • Solution handling robot mixes the crystallisation chemicals from stock solutions and prepares the crystallisation plate.
  • Nanodispensing robot sets up the crystallisation drops by mixing the protein with an aliquot of the well solution.
  • Robotic plate mover moves plates to the microscope according to their imaging schedule and digital images of each drop are stored in the database.

Hamilton Microlab STAR

  • Robot mixes the crystallisation chemicals from as many as 60 stock solutions at a time. The robot can accurately handle many types of liquids from alcohols to viscous PEG solutions, down to volumes as low as 2 µl. All crystallisation chemicals are first pipetted into a deep well block at 1-2 ml volume, mixed and then aliquoted to the crystallisation plate.

TTP Labtech’s mosquito LCP

  • TTP Labtech’s mosquito LCP® liquid handling  provides you with precise and repeatable nanolitre pipetting, every time, irrespective of liquid viscosity or environmental conditions.  It can pipette accurately down to 50 nl volumes, but we prefer to use a minimum of 100 nl of protein and 100 nl of well solution. During the drop dispense step, the plate is covered to minimize evaporation. Immediately after building of the setup is complete, the plate is sealed with transparent film.
  • The LCP technique for crystallising membrane proteins can be difficult and time-consuming to set up by hand as it utilises highly viscous lipid mesophases to reconstitute proteins. TTP LabTech has overcome these problems with mosquito LCP, a dedicated pipetting instrument for automated LCP screening set-up.
  • Using a positive displacement syringe with automated tip positioning, mosquito LCP provides accurate and repeatable dispensing of the LCP drops.

Minstrel  DT UV – Protein Crystal Imaging System  at the room temperature 

  • The Minstrel DT UV from Rigaku is an ultraviolet and visible crystal imaging and protein crystal monitoring system. This robotic instrument is a major advance over previous visible light microscopy technology because its UV technology can find crystals in complex drops and easily distinguish protein crystals from non-protein crystals (such as salt).

Xtal Focus – Protein Crystal Imaging Systems  at the cool room

  • The robotic handler feeds plates to the Xtal Focus imager as determined by a preprogrammed schedule.  The plate history and all images are stored into the database.  

PiXray program

  • Allows users to remotely view and score their images over the web or across other platforms such as Mac or PC. Link to the viewer here.
  • Our service is open for all users
  • Our facility can be used ONLY for samples of the biosafety level 1 (e.g. human pathogens, live viruses, toxins and radioactive material are not accepted).
  • We serve on a first-come-first-served basis
  • Register your project by filling the user registration form (link to the eForm coming soon) for approval (feasibility, technical checking);
  • Register as an Instruct-ERIC user network (link);
  • Users agree to acknowledge the crystallization infrastructure upon publishing the results with the following text: " The authors acknowledge the use of Instruct-HiLIFE Crystallization unit (University of Helsinki, Biocenter Finland, and Instruct-FI).”
  • Please send the bibliography to bi-crystallisation[at]helsinki.fi.

Deep Well Block Crystallisation Reagents:
From facility screen selection/grid screen reagents 60€

Custom sparse matrix/random screen solutions (outside of our standard selection ) 100€ *

  • 96 deep well format for manual crystallisation setup
  • Standard or custom screen chemicals
  • Price does not include shipping

You can order any screen from our selection of standard screens. Alternatively, you can design your own screen solutions and order them as customised stock solutions for manual pipetting.

*please inquire about service availability

Sample optimisation and protein stability measurements with Thermofluor 30€

Highly recommended as a first step before crystallisation

  • Measure the thermostability of your protein based on fluorescent dye binding
  • Do the full buffer and salt screen (96 wells format)

Sample optimisation with HPLC-MALLS 30€ /run    

  • Analysis of sample monodispersity and molecular weight by analytical size exclusion chromatography and static light scattering with microliter volumes.

Protein Nanodrop Crystallisation With Standard Screen Chemicals, 50€

The price includes:

  • Crystallisation plate
  • Crystallisation screen preparation: 96/192/288 protein drops in 96 different conditions
  • Scheduled imaging in +20 C or +4 C
  • Plate storage for six months
  • Remote access to all images

Protein Nanodrop Crystallisation With Optimisation Screen Chemicals, 60€

Includes all service as in standard crystallisation experiment

  • Crystalllisation with Customize Grid also includes the corresponding crystallisation solutions in a deep well block
  • Simple screen is composed of max 10 chemicals and water

Chemicals if not in Standard Sets, + 10€

Hampton Additives, 10€

  • Added to the crystallisation setup of your choice

Crystallisation screen with LCP, 75€

The price includes:

  • Nano-drop setup is done by using  mosquito LCP 
  • LaminexTM UV Plastic Base 100 Micron  
  • LaminexTM UV Plastic Cover   http://www.moleculardimensions.com
  • Scheduled imaging in  +20 C
  • Plate storage for six months

Crystallisation screen with seeding, 70€

The price includes:

  • Preparation of seeding solution with the Seed Bead (Hampton Research, HR2-320)
  • Nano-drop setup with Mosquito robot
  • Scheduled imaging
  • Plate storage for 6 months
  • Remote access to all images

 

Sitting or hanging drop 24-well plates, 8-16€

The price includes:

  • A plate
  • Coverslips/tape
  • Imaging according to schedule
  • Access to all images

 

A new temperature-screening system (Thermo-screen), 60€

The price includes:

  • Crystallisation plate
  • Crystallisation screen preparation: 96/192 drops. 8 different conditions over 12 temperature points
  • Manual imaging at +20 C according to agreed schedule
  • Remote access to all images

Crystal diffraction screening and data collection at synchrotron (+shipping fees)*
The service includes:

  • Fishing and cryoprotecting the crystals with oil
  • Transportation to and from the synchrotron
  • Data collection and primary automatic analysis

*please inquire about pricing

In situ plate data collection at synchrotron*

The price includes:

  • Screening of a plate at Diamond (UK) or ESRF (France)
  • Transportation to and from the synchrotron
  • Data collection and primary automatic analysis

*please inquire about pricing

 

Technical or Expert work: 30€ /hour

All prices are VAT 0% and apply to academic users only.
Industry / users outside Finland, please contact for information on pricing.

Prices are valid from 30.03.2016.

  • Kolodziejczyk R, Mikula KM, Kotila T, Postis VLG, Jokiranta TS, Goldman A, Meri T. Crystal structure of a tripartite complex between C3dg, C-terminal domains of factor H and OspE of Borrelia burgdorferi. PLoS One. 2017 Nov 30;12(11):e0188127. doi: 10.1371/journal.pone.0188127.

  • Iwaï H, Mikula KM, Oeemig JS, Zhou D, Li M, Wlodawer A. Structural Basis for the Persistence of Homing Endonucleases in Transcription Factor IIB Inteins. J Mol Biol. 2017 Dec 8;429(24):3942-3956. doi: 10.1016/j.jmb.2017.10.016.

  • Leppänen VM, Saharinen P, Alitalo K. Structural basis of Tie2 activation and Tie2/Tie1 heterodimerization. Proc Natl Acad Sci U S A. 2017 Apr 25;114(17):4376-4381. doi: 10.1073/pnas.1616166114.

  • Li KM, Wilkinson C, Kellosalo J, Tsai JY, Kajander T, Jeuken LJ, Sun YJ, Goldman A. Membrane pyrophosphatases from Thermotoga maritima and Vigna radiata suggest a conserved coupling mechanism. Nat Commun. 2016 Dec 6;7:13596. doi: 10.1038/ncomms13596.

  • Paatero A, Rosti K, Shkumatov AV, Sele C, Brunello C, Kysenius K, Singha P, Jokinen V, Huttunen H, Kajander T. Crystal Structure of an Engineered LRRTM2 Synaptic Adhesion Molecule and a Model for Neurexin Binding. Biochemistry. 2016 Feb 16;55(6):914-26. doi: 10.1021/acs.biochem.5b00971. Epub 2016 Feb 3. 

  • Guryanov SG, Liljeroos L, Kasaragod P, Kajander T, Butcher SJ. Crystal Structure of the Measles Virus Nucleoprotein Core in Complex with an N-Terminal Region of Phosphoprotein. J Virol. 2015 Dec 30;90(6):2849-57. doi: 10.1128/JVI.02865-15.

  • Bhattacharjee A, Reuter S, Trojnár E, Kolodziejczyk R, Seeberger H, Hyvärinen S, Uzonyi B, Szilágyi Á, Prohászka Z, Goldman A, Józsi M, Jokiranta TS. The major autoantibody epitope on factor H in atypical hemolytic uremic syndrome is structurally different from its homologous site in factor H-related protein 1, supporting a novel model for induction of autoimmunity in this disease. J Biol Chem. 2015 Apr 10;290(15):9500-10. doi: 10.1074/jbc.M114.630871. Epub 2015

  • Rosti K, Goldman A, Kajander T. Solution structure and biophysical characterization of the multifaceted signalling effector protein growth arrest specific-1. BMC Biochem. 2015 Feb 28;16:8. doi: 10.1186/s12858-015-0037-6.

  • Aranko AS, Oeemig JS, Zhou D, Kajander T, Wlodawer A, Iwaï H. Structure-based engineering and comparison of novel split inteins for protein ligation. Mol Biosyst. 2014 May;10(5):1023-34. doi: 10.1039/c4mb00021h.

  • Aranko AS, Oeemig JS, Kajander T, Iwaï H. Intermolecular domain swapping induces intein-mediated protein alternative splicing. Nat Chem Biol. 2013 Oct;9(10):616-22. doi: 10.1038/nchembio.1320. Epub 2013 Aug 25.

  • Happonen LJ, Oksanen E, Liljeroos L, Goldman A, Kajander T, Butcher SJ. The structure of the NTPase that powers DNA packaging into Sulfolobus turreted icosahedral virus 2. J Virol. 2013 Aug;87(15):8388-98. doi: 10.1128/JVI.00831-13. Epub 2013 May 22.

  • Bhattacharjee A, Oeemig JS, Kolodziejczyk R, Meri T, Kajander T, Lehtinen MJ, Iwaï H, Jokiranta TS, Goldman A. Structural basis for complement evasion by Lyme disease pathogen Borrelia burgdorferi. J Biol Chem. 2013 Jun 28;288(26):18685-95. doi: 10.1074/jbc.M113.459040.

  • Leppänen VM, Tvorogov D, Kisko K, Prota AE, Jeltsch M, Anisimov A, Markovic-Mueller S, Stuttfeld E, Goldie KN, Ballmer-Hofer K, Alitalo K. Structural and mechanistic insights into VEGF receptor 3 ligand binding and activation. Proc Natl Acad Sci U S A. 2013 Aug 6;110(32):12960-5. doi: 10.1073/pnas.1301415110.

  • Pihlajamaa T, Kajander T, Knuuti J, Horkka K, Sharma A, Permi P. Structure of Plasmodium falciparum TRAP (thrombospondin-related anonymous protein) A domain highlights distinct features in apicomplexan von Willebrand factor A homologues. Biochem J. 2013 Mar 15;450(3):469-76. doi: 10.1042/BJ20121058.

  • Kellosalo J, Kajander T, Honkanen R, Goldman A. Crystallization and preliminary X-ray analysis of membrane-bound pyrophosphatases. Mol Membr Biol. 2013 Feb;30(1):64-74. doi: 10.3109/09687688.2012.712162. Epub 2012 Aug 13.

  • Kellosalo J, Kajander T, Kogan K, Pokharel K, Goldman A. The structure and catalytic cycle of a sodium-pumping pyrophosphatase. Science. 2012 Jul 27;337(6093):473-6. doi: 10.1126/science.1222505.

  • Oeemig JS, Zhou D, Kajander T, Wlodawer A, Iwaï H. NMR and crystal structures of the Pyrococcus horikoshii RadA intein guide a strategy for engineering a highly efficient and promiscuous intein. J Mol Biol. 2012 Aug 3;421(1):85-99. doi: 10.1016/j.jmb.2012.04.029. Epub 2012 May 2.

  • Kajander T, Kuja-Panula J, Rauvala H, Goldman A. Crystal structure and role of glycans and dimerization in folding of neuronal leucine-rich repeat protein AMIGO-1. J Mol Biol. 2011 Nov 11;413(5):1001-15. doi: 10.1016/j.jmb.2011.09.032. Epub 2011 Sep 29.