CSSB Centre for Structural Systems Biology
Home Facilities HTX

High-Throughput Crystallisation

  • Next to beamlines at PETRA III.
  • Equipped for initial and customized screening.
  • CrystalDirect technology and automated crystal harvesting.


Available Instruments

  • Mosquito LCP (two units)
  • Scorpion Screen Formulator
  • Biomec 4000 (liquid handling platform)
  • Rock Imager at 4 and 19 °C
  • Automatic crystal harvester (CrystalDirect)



 The HTX facility offers a variety of services related to protein crystallisation:

  • Automatic setup of crystallization trays using Mosquito-LCP
  • Low volume crystallisation screening for sitting and hanging drop experiments
  • >30 commercial screens available
  • Crystal condition optimisation
  • Large storage capacity at 19ºC and 4ºC
  • Specialised Crystal information management system (CRIMS) to schedule and monitor experiments.
  • Automated image acquisition (Vis/UV) and remote access environment for the user via the CRIMS system.


Further Information

Our high-throughput crystallization laboratory offers initial crystallization screens from various suppliers as well as customized screens for optimization of initial hits, both suitable for soluble and membrane proteins. Drops are set with nanolitre dispensing robots; the TTP’s MOSQUITO equipped with an LCP (Lipidic Cubic Phase) module. Online observation of the plates is possible via the Crystallization Information Management System (CRIMS), which makes results available to users in real-time, along with all experimental parameters. We offer the CrystalDirect® technology, able to harvest protein crystals from 96-well CrystalDirectTM plates by means of laser photoablation. We facilitate access to Biological SAXS measurements with near-real time outputs of structural parameters and low-resolution solution-state structures in collaboration with the SAXS group.

Access & Team


The facility is a fee-for-service (non-profit) technology platform operated by EMBL. We provide support and expertise for local scientists, the international research community and users from industry.

All users must follow a safety training before working in our laboratories. Complete the SPC safety briefing and examination before your visit though SMIS. Please go to the Safety tab and select "Standard Training." All users are required to undergo training before access to the individual instruments is granted.

Booking and more information about crystallisation can be found on our SPC crystallisation platform (CRIMS): https://htx.embl-hamburg.de

Please get in touch with us to discuss your specific needs spc@embl-hamburg.de.

Our acknowledgement policy

Please acknowledge any substantial contributions of the SPC Facility to your research in publications. Please state the following in the acknowledgement section of your publication: “We acknowledge technical support by the SPC facility at EMBL Hamburg”.

Please don't forget to let us know when you publish papers that acknowledge us. This will help us keep track and to justify the existence of the facility to funding bodies.



Facility Head

Dr. Maria Garcia Alai


Research Technician

Christian Guenther
Phone:+49 40 8998 02210



CSSB Centre for Structural Systems Biology
c/o Deutsches Elektronen-Synchrotron DESY
Notkestraße 85, Building 15
D-22607 Hamburg

Facility Operator: European Molecular Biology Laboratory (EMBL)



Bücker R, Seuring C, Cazey C, Veith K, García-Alai M, Grünewald K, Landau M (2022) The Cryo-EM structures of two amphibian antimicrobial cross-β amyloid fibrils. Nat Commun. 13(1):4356. doi: 10.1038/s41467-022-32039-z

Burastero O, Defelipe LA, Gola G, Tateosian NL, Lopez ED, Martinena CB, Arcon JP, Traian MD, Wetzler DE, Bento I, Barril X, Ramirez J, Marti MA, Garcia-Alai MM, Turjanski AG (2022) Cosolvent Sites-Based Discovery of <i>Mycobacterium Tuberculosis</i> Protein Kinase G Inhibitors. Journal of medicinal chemistry. 65(14):9691-9705. doi:10.1021/acs.jmedchem.1c02012

Niebling S, Veith K, Vollmer B, Lizarrondo J, Burastero O, Schiller J, Struve García A, Lewe P, Seuring C, Witt S, García-Alai M (2022) Biophysical Screening Pipeline for Cryo-EM Grid Preparation of Membrane Proteins. Front. Mol. Biosci. 9:882288. doi: 10.3389/fmolb.2022.882288

Kopicki JD, Saikia A, Niebling S, Günther C, Anjanappa R, Garcia-Alai M, Springer S, Uetrecht C (2022) Opening opportunities for Kd determination and screening of MHC peptide complexes. Commun Biol. 5(1):488. doi: 10.1038/s42003-022-03366-0.


Burastero O, Niebling S, Defelipe LA, Gunther C, Struve A, Alai MMG (2021) eSPC: an online data-analysis platform for molecular biophysics. Acta Crystallographica Section D Structural Biology, 77, 1241{1250 doi:10.1107/S2059798321008998.

Bucher M, Niebling S, Han Y, Molodenskiy D, Nia FH, Kreienkamp HJ, Svergun D, Kim E, Kostyukova AS, Kreutz MR, Mikhaylova M (2021) Autism-associated SHANK3 missense point mutations impact conformational uctuations and protein turnover at synapses.eLife,10 e66165 doi: 10.7554/eLife.66165

Lorenzo R, Defelipe LA, Aliperti L, Niebling S, Custódio TF, Löw C, Schwarz JJ, Remans K, Craig PO, Otero LH, Klinke S, García-Alai M, Sánchez IE, Alonso LG (2021) Deamidation drives molecular aging of the SARS-CoV-2 spike protein receptor-binding motif. J Biol Chem.101175. doi: 10.1016/j.jbc.2021.101175.

López-Méndez B, Baron B, Brautigam CA, Jowitt TA, Knauer SH, Uebel S, Williams MA, Sedivy A, Abian O, Abreu C, Adamczyk M, Bal W, Berger S, Buell AK, Carolis C, Daviter T, Fish A, Garcia-Alai M, Guenther C, Hamacek J, Holková J, Houser J, Johnson C, Kelly S, Leech A, Mas C, Matulis D, McLaughlin SH, Montserret R, Nasreddine R, Nehmé R, Nguyen Q, Ortega-Alarcón D, Perez K, Pirc K, Piszczek G, Podobnik M, Rodrigo N, Rokov-Plavec J, Schaefer S, Sharpe T, Southall J, Staunton D, Tavares P, Vanek O, Weyand M, Wu D (2021) Reproducibility and accuracy of microscale thermophoresis in the NanoTemper Monolith: a multi laboratory benchmark study. Eur Biophys J. 50(3-4):411-427. doi:10.1007/s00249-021-01532-6.

de Marco A, Berrow N, Lebendiker M, Garcia-Alai M, Knauer SH, Lopez-Mendez B, Matagne A, Parret A, Remans K, Uebel S, Raynal B (2021) Quality control of protein reagents for the improvement of research data reproducibility. Nat Commun.12(1):2795. doi:10.1038/s41467-021-23167-z.

Niebling S, Burastero O, Bürgi J, Günther C, Defelipe LA, Sander S, Gattkowski E, Anjanappa R, Wilmanns M, Springer S, Tidow H, García-Alai M (2021) FoldAffinity: binding affinities from nDSF experiments. Sci Rep. 11(1):9572. doi:10.1038/s41598-021-88985-z.

Berrow N, de Marco A, Lebendiker M, Garcia-Alai M, Knauer SH, Lopez-Mendez B, Matagne A, Parret A, Remans K, Uebel S, Raynal B (2021) Quality control of purified proteins to improve data quality and reproducibility: results from a large-scale survey. Eur Biophys J. 50(3-4):453-460. doi:10.1007/s00249-021-01528-2.

Winkel Missel J, Salustros N, Ramos Becares E, Hyld Steffen J, Gerdt Laursen A, Struve Garcia A, Garcia-Alai MM, Kolar Č, Gourdon P, Gotfryd K (2021) Cyclohexyl-α maltoside as a highly efficient tool for membrane protein studies. Current Research in Structural Biology. https://doi.org/10.1016/j.crstbi.2021.03.002.

Lizarrondo J, Klebl DP, Niebling S, Abella M, Schroer MA, Mertens HDT, Veith K, Thuenauer R, Svergun DI, Skruzny M, Sobott F, Muench SP, Garcia-Alai MM (2021) Structure of the endocytic adaptor complex reveals the basis for efficient membrane anchoring during clathrin-mediated endocytosis. Nat Commun.12(1):2889. doi: 10.1038/s41467-021-23151-7.

Günther S, Reinke PYA, Fernández-García Y, Lieske J, Lane TJ, Ginn HM, Koua FHM, Ehrt C, Ewert W, Oberthuer D, Yefanov O, Meier S, Lorenzen K, Krichel B, Kopicki JD, Gelisio L, Brehm W, Dunkel I, Seychell B, Gieseler H, Norton-Baker B, Escudero-Pérez B, Domaracky M, Saouane S, Tolstikova A, White TA, Hänle A, Groessler M, Fleckenstein H, Trost F, Galchenkova M, Gevorkov Y, Li C, Awel S, Peck A, Barthelmess M, Schluenzen F, Lourdu Xavier P, Werner N, Andaleeb H, Ullah N, Falke S, Srinivasan V, França BA, Schwinzer M, Brognaro H, Rogers C, Melo D, Zaitseva-Doyle JJ, Knoska J, Peña-Murillo GE, Mashhour AR, Hennicke V, Fischer P, Hakanpää J, Meyer J, Gribbon P, Ellinger B, Kuzikov M, Wolf M, Beccari AR, Bourenkov G, von Stetten D, Pompidor G, Bento I, Panneerselvam S, Karpics I, Schneider TR, Garcia-Alai MM, Niebling S, Günther C, Schmidt C, Schubert R, Han H, Boger J, Monteiro DCF, Zhang L, Sun X, Pletzer-Zelgert J, Wollenhaupt J, Feiler CG, Weiss MS, Schulz EC, Mehrabi P, Karničar K, Usenik A, Loboda J, Tidow H, Chari A, Hilgenfeld R, Uetrecht C, Cox R, Zaliani A, Beck T, Rarey M, Günther S, Turk D, Hinrichs W, Chapman HN, Pearson AR, Betzel C, Meents A. (2021) X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease. Science. 2021 Apr 2:eabf7945. doi: 10.1126/science.abf7945.


Heidemann J, Kölbel K, Konijnenberg A, Van Dyck J, Garcia-Alai M, Meijers R, Sobott F, Uetrecht C. (2020) Further insights from structural mass spectrometry into endocytosis adaptor protein assemblies. Int J Mass Spectrom. 2019 Oct 18;447:116240. doi: 10.1016/j.ijms.2019.116240.

Anjanappa R, Garcia-Alai M, Kopicki JD, Lockhauserbäumer J, Aboelmagd M, Hinrichs J, Nemtanu IM, Uetrecht C, Zacharias M, Springer S, Meijers R (2020) Structures of peptide-free and partially loaded MHC class I molecules reveal mechanisms of peptide selection. Nat Commun. 11;11(1):1314. doi: 10.1038/s41467-020-14862-4.


Saini SK, Tamhane T, Anjanappa R, Saikia A, Ramskov S, Donia M, Svane IM, Jakobsen SN, Garcia-Alai M, Zacharias M, Meijers R, Springer S, Hadrup SR (2019) Empty peptide-receptive MHC class I molecules for efficient detection of antigen-specific T cells. Sci Immunol 410.1126/sciimmunol.aau9039 doi: 10.1126/sciimmunol.aau9039

Moritz A, Anjanappa R, Wagner C, Bunk S, Hofmann M, Pszolla G, Saikia A, Garcia-Alai M, Meijers R, Rammensee HG, Springer S, Maurer D (2019) High-throughput peptide-MHC complex generation and kinetic screenings of TCRs with peptide-receptive HLA-A*02:01 molecules. Sci Immunol 410.1126/sciimmunol.aav0860. doi: 10.1126/sciimmunol.aav0860.

Kotov V, Bartels K, Veith K, Josts I, Subhramanyam UKT, Gunther C, Labahn J, Marlovits TC, Moraes I, Tidow H, Low C, Garcia-Alai MM (2019) High-throughput stability screening for detergent-solubilized membrane proteins. Sci Rep 9: 10379.doi: 10.1038/s41598-019-46686-8

Gattkowski E, Johnsen A, Bauche A, Möckl F, Kulow F, Garcia Alai M, Rutherford TJ, Fliegert R, Tidow H. (2019) Novel CaM-binding motif in its NudT9H domain contributes to temperature sensitivity of TRPM2. Biochim Biophys Acta Mol Cell Res. 2019 Jul;1866(7):1162-1170. doi: 10.1016/j.bbamcr.2018.12.010.


Garcia-Alai MM, Heidemann J, Skruzny M, Gieras A, Mertens HDT, Svergun DI, Kaksonen M, Uetrecht C, Meijers R (2018) Epsin and Sla2 form assemblies through phospholipid interfaces. Nat Commun 9: 328 doi: 10.1038/s41467-017-02443-x

Molina IG, Josts I, Almeida Hernandez Y, Esperante S, Salgueiro M, Garcia Alai MM, de Prat-Gay G, Tidow H. (2018) Structure and stability of the Human respiratory syncytial virus M 2-1 RNA-binding core domain reveals a compact and cooperative folding unit. Acta Crystallogr F Struct Biol Commun. 2018 Jan 1;74(Pt 1):23-30. doi: 10.1107/S2053230X17017381.




The HTX facility is involved in the following research projects:

X-ray based screen of drugs against SARS-CoV-2
The project aims at performing high-throughput X-ray crystallographic screening experiments of several thousand compounds in complex with protein targets at the PETRA III synchrotron, to identify potential drug candidates, which will be subsequently tested in protein activity assays and finally virus cell cultures. The PC and HTX facilities will be used to further characterize drug/target complexes biophysically.
CSSB PC and HTX facilities: Maria Garcia Alai (EMBL)
Scientific Leadership: Alke Meents (DESY)