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X-ray crystallography

The most widely used structural method for the determination of high-resolution structures of biological samples is X-ray crystallography.

Protein Crystallization. Our Institute is equipped with a Tecan robot for high throughput automated screening of crystal growth in 96-well format and volumes as small as 200 nL. For a new target protein, we routinely screen up to a thousand different crystallization conditions, varying several parameters such as pH, ionic strength and precipitating agents. The initial crystals are then optimized either with automated or manual set ups to obtain single crystals for the X‑ray diffraction experiments.

Documentation. A digital documentation system is in operation for the evaluation and recording of results.

We have an in-house rotating anode generator for single crystal X-ray diffraction experiments. The computer infrastructure in ICS-6 is equipped with a variety of crystallographic software required for the data analysis. Additionally, we have regular access to the beamlines at Deutsches Elektronen Synchrotron (DESY) of the Helmholtz Association in Hamburg and to the European Synchrotron Radiation Facility (ESRF) in Grenoble, France.

These facilities are available to researchers within the framework of collaborative projects.

For further information see:

Arbeitsgruppe Batra-Safferling
Arbeitsgruppe Weiergräber

Structure Gallery

Kovacic F, Granzin J, Wilhelm S, Kojic-Prodic B, Batra-Safferling R, Jaeger KE

Structural and Functional Characterisation of TesA - A Novel Lysophospholipase A from Pseudomonas aeruginosa.
PLoS One 8, e69125 (2013)


Granzin J, Cousin A, Weirauch M, Schlesinger R, Büldt G, Batra-Safferling 

Crystal structure of p44, a constitutively active splice variant of visual arrestin.
J Mol Biol. 416, 611-8 (2012)



Circolone, F, Granzin, J, Jentzsch, K, Drepper, T, Jaeger, KE, Willbold, D, Krauss, U, Batra-Safferling, R

Structural basis for the slow dark recovery of a full-length LOV protein from Pseudomonas putida.
J.Mol.Biol. 417, 362-374 (2012)


  • Amariei DA, Pozhydaieva N, David B, Schneider P, Classen T, Gohlke H, Weiergräber OH, Pietruszka J 
    Enzymatic C3-Methylation of Indoles Using Methyltransferase PsmD─Crystal Structure, Catalytic Mechanism, and Preparative Applications 
    ACS Catal 12, 14130-14139 (2022) 
  • Brown H, Chung M, Üffing A, Batistatou N, Tsang T, Doskocil S, Mao W, Willbold D, Bast RC Jr, Lu Z, Weiergräber OH, Kritzer JA 
    Structure-Based Design of Stapled Peptides That Bind GABARAP and Inhibit Autophagy 
    J Am Chem Soc 144, 14687-14697 (2022) 
  • Florian Bleffert, Joachim Granzin, Muttalip Caliskan, Stephan N Schott-Verdugo, Meike Siebers, Björn Thiele, Laurence Rahme, Sebastian Felgner, Peter Dörmann, Holger Gohlke* , Renu Batra-Safferling*, Karl-Erich Jaeger, Filip Kovacic* 
    Structural, mechanistic, and physiological insights into phospholipase A-mediated membrane phospholipid degradation in Pseudomonas aeruginosa. 
    eLife 11, e72824 (2022) 
  • Hemmer S, Schulte M, Knieps-Grünhagen E, Granzin J, Willbold D, Jaeger KE, Batra-Safferling R, Panwalkar V, Krauss U. 
    Residue alterations within a conserved hydrophobic pocket influence light, oxygen, voltage photoreceptor dark recovery. 
    Photochem Photobiol Sci , (2022) 
  • Huwa N, Weiergräber OH, Fejzagić AV, Kirsch C, Schaffrath U, Classen T 
    The Crystal Structure of the Defense Conferring Rice Protein OsJAC1 Reveals a Carbohydrate Binding Site on the Dirigent-like Domain 
    Biomolecules 12, 1126 (2022) 
  • Rosenbach H, Span I 
    Obtaining Crystals of Nucleic Acids in Complex with the Protein U1A Using the Soaking Method 
    Methods in Molecular Biology 2439, 105-115 (2022) 
  • Weiergräber OH, Petrović D, Kislat A, Pattky M, Fabig J, Batra-Safferling R, Schulte am Esch J, Hänel K, Huhn C, Strodel B, Homey B, Willbold D 
    Structure and Dynamics of Human Chemokine CCL16—Implications for Biological Activity 
    Biomolecules 12, 1588 (2022) 
  • Arinkin V, Granzin J, Krauss U, Jaeger KE, Willbold D, Batra-Safferling R. 
    Structural determinants underlying the adduct lifetime in the LOV proteins of Pseudomonas putida. 
    FEBS J 288(16), 4955-4972 (2021) 
  • Freischem S, Grimm I, López-Pérez A, Willbold D, Klenke B, Vuong C, DingleyAJ, Weiergräber OH 
    Interaction Mode of the Novel Monobactam AIC499 Targeting Penicillin Binding Protein 3 of Gram-Negative Bacteria 
    Biomolecules 11, 1057 (2021) 
  • Röllen K, Granzin J, Remeeva A, Davari MD, Gensch T, Nazarenko VV, Kovalev K, Bogorodskiy A, Borshchevskiy V, Hemmer S, Schwaneberg U, Gordeliy V, Jaeger KE, Batra-Safferling R, Gushchin I, Krauss U. 
    The molecular basis of spectral tuning in blue- and red-shifted flavin-binding fluorescent proteins. 
    J Biol Chem 296, 100662 (2021) 
  • Patricia Rodríguez-Maciá, Lisa M. Galle, Ragnar Bjornsson, Christian Lorent, Ingo Zebger, Yoshitaka Yoda, Stephen P. Cramer, Serena DeBeer, Ingrid Span and James A. Birrell 
    Caught in the Hinact: Crystal Structure and Spectroscopy Reveal a Sulfur Bound to the Active Site of an O2-stable State of [FeFe] Hydrogenase 
    Angewandte Chemie International Edition 59, 2-11 (2020) 
  • Rosenbach H, Victor J, Borggräfe J, Biehl R, Steger G, Etzkorn M, Span I. 
    Expanding crystallization tools for nucleic acid complexes using U1A protein variants 
    Journal of Structural Biology 210, 107480 (2020) 
  • Stadler AM, Granzin J, Cousin A, Batra-Safferling R. 
    Phosphorylated peptide of G protein-coupled receptor induces dimerization in activated arrestin. 
    Scientific Reports 10, 10938 (2020) 
  • Bleffert F, Granzin J, Gohlke H, Batra-Safferling R, Jaeger KE, Kovacic F 
    Pseudomonas aeruginosa esterase PA2949, a bacterial homolog of the human membrane esterase ABHD6: expression, purification and crystallization. 
    Acta Crystallography F75, 270-277 (2019) 
  • Kukuk L, Dingley AJ, Granzin J, Nagel-Steger L, Thiagarajan-RosenkranzP, Ciupka D, Hänel K, Batra-Safferling R, Pacheco V, Stoldt M, PfefferK, Beer-Hammer S, Willbold D, Koenig BW 
    Structure of the SLy1 SAM homodimer reveals a new interface for SAM domain self-association 
    Scientific Reports 9, 54 (2019) 
  • Schwarten M, Weiergräber OH, Petrović D, Strodel B, Willbold D 
    Structural Studies of Autophagy-Related Proteins 
    Methods Mol Biol 1880, 17-56 (2019) 
  • Fettweiss T, Röllen K, Granzin J, Reiners O, Endres S, Drepper T, Willbold D, Jaeger KE, Batra-Safferling R*, Krauss U* 
    Mechanistic Basis of the Fast Dark Recovery of the Short LOV Protein DsLOV from Dinoroseobacter shibae. 
    Biochemistry 57, 4833–4847 (2018) 
  • Röllen, K.; Granzin, J.; Batra-Safferling, R*.; Stadler, A.M*. 
    Small-angle X-ray scattering study of the kinetics of light-dark transition in a LOV protein 
    PLoS One 13(7):e0200746, (2018) 
  • Arinkin V, Granzin J, Röllen K, Krauss U, Jaeger KE, Willbold D, Batra-Safferling R. 
    Structure of a LOV protein in apo-state and implications for construction of LOV-based optical tools 
    Scientific Reports 7(42971), (2017) 
  • Batra-Safferling R and Granzin J.  
    The Structure of the Polar Core Mutant R175E and Its Functional Implications.  
    The Structural Basis Of Arrestin Functions, Vsevolod V. Gurevich (Editor); Springer International Publishing Chapter 11, 143-158 (2017) 
    ISBN: 978-3-319-57552-0 
  • Gushchin I, Melnikov I, Polovinkin V, Ishchenko A, Yuzhakova A, Buslaev P, Bourenkov G, Grudinin S, Round E, Balandin T, Borshchevskiy V, Willbold D, Leonard G, Büldt G, Popov A, Gordeliy V. 
    Mechanism of transmembrane signaling by sensor histidine kinases. 
    Science 356, eaah6345 (2017) 
  • Nikolaev M, Round E, Gushchin I, Polovinkin V, Balandin T, Kuzmichev P, Shevchenko V, Borshchevskiy V, Kuklin A, Round A, Bernhard F, Willbold D, Büldt G, Gordeliy V.  
    Integral membrane proteins can be crystallized directly from nanodiscs. 
    Cryst. Growth Des. 17, 945-948 (2017) 
  • Schlesinger R, Cousin A, Granzin J, Batra-Safferling R.  
    Expression and purification of arrestin in yeast Saccharomyces cerevisiae. 
    Methods Cell Biol 142, 159-172 (2017) 
  • Volkov O, Kovalev K, Polovinkin V, Borshchevskiy V, Bamann C, Astashkin R, Marin E, Popov A, Balandin T, Willbold D, Büldt G, Bamberg E, Gordeliy V 
    Structural insights into ion conduction by channelrhodopsin 2 
    Science 358, eaan8862, (2017) 
  • Weiergräber OH, Schwarten M, Strodel B, Willbold D.  
    Investigating Structure and Dynamics of Atg8 Family Proteins. 
    Methods Enzymol 587, 115-142 (2017) 
  • Röllen K, Granzin J, Panwalkar V, Arinkin V, Rani R, Hartmann R, Krauss U, Jaeger KE, Willbold D, Batra-Safferling R. 
    Signaling States of a Short Blue-Light Photoreceptor Protein PpSB1-LOV Revealed from Crystal Structures and Solution NMR Spectroscopy. 
    J Mol Biol. 428, 3721 - 3736 (2016) 
  • Endres S, Granzin J, Circolone F, Stadler A, Krauss U, Drepper T, Svensson V, Knieps-Grünhagen E, Wirtz A, Cousin A, Tielen P, Willbold D, Jaeger K-E, Batra-Safferling R 
    Structure and function of a short LOV protein from the marine phototrophic bacterium Dinoroseobacter shibae. 
    BMC Microbiology 15, 30 (2015) 
  • Granzin J, Stadler A, Cousin A, Schlesinger R, Batra-Safferling R 
    Structural evidence for the role of polar core residue Arg175 in arrestin activation. 
    Scientific Reports 5, 15808 (2015) 
  • Gushchin I, Shevchenko V, Polovinkin V, Kovalev K, Alekseev A, Round E, Borshchevskiy V, Balandin T, Popov A, Gensch T, Fahlke C, Bamann C, Willbold D, Büldt G, Bamberg E, Gordeliy V 
    Crystal structure of a light-driven sodium pump. 
    Nat. Struct. Mol. Biol. 22, 390-395 (2015) 
  • Ma P, Schillinger O, Schwarten M, Lecher J, Hartmann R, Stoldt M, Mohrlüder J, Olubiyi O, Strodel B, Willbold D, Weiergräber OH 
    Conformational Polymorphism in Autophagy-Related Protein GATE-16 
    Biochemistry 54, 5469-5479 (2015) 
  • Ma P, Xue Y, Coquelle N, Haller JD, Yuwen T, Ayala I, Mikhailovskii O, Willbold D, Colletier J-P, Skrynnikov NR, Schanda P 
    Observing the overall rocking motion of a protein in a crystal. 
    Nat. Commun. 6, 8361 (2015) 
  • Michel M, Schwarten M, Decker C, Nagel-Steger L, Willbold D, Weiergräber OH 
    The mammalian autophagy initiator complex contains 2 HORMA domain proteins 
    Autophagy 11, 2300-2308 (2015) 
  • Polovinkin V, Gushchin I, Sintsov M, Round E, Balandin T, Chervakov P, Schevchenko V, Utrobin P, Popov A, Borshchevskiy V, Mishin A, Kuklin A, Willbold D, Chupin V, Popot JL, Gordeliy V 
    High-Resolution Structure of a Membrane Protein Transferred from Amphipol to a Lipidic Mesophase 
    J. Membr. Biol. 247, 997-1004 (2014) 
  • Kalisman N, GF Schröder, M Levitt 
    The Crystal Structures of the Eukaryotic Chaperonin CCT Reveal its Functional Partitioning 
    Structure 21, 540 (2013) 
  • Brunger AT, D Das, AM Deacon, J Grant, TC Terwilliger, RJ Read, PD Adams, M Levitt and GF Schröder 
    Application of DEN-Refinement And Automated Model-Building To A Difficult Case Of Molecular Replacement Phasing: The Structure Of A Putative Succinyl-Diaminopimelate Desuccinylase From Corynebacterium Glutamicum. 
    Acta Cryst. D 68, 391 (2012) 
  • Brunger AT, PD Adams, P Fromme, R Fromme, M Levitt, and GF Schröder 
    Improving the accuracy of macromolecular structure refinement at 7 Å resolution. 
    Structure 20(6), 957 (2012) 
  • O'Donovan DJ, I Stokes-Rees, Y Nam, S Blacklow, GF Schröder, AT Brunger, Piotr Sliz 
    A grid-enabled web service for low-resolution crystal structure refinement. 
    Acta Cryst. D 68, 268 (2012) 
  • Gao S, von der Malsburg A, Dick A, Faelber K, Schröder GF, Haller O, Kochs G, Daumke O 
    Three domain architecture of dynamin-like MxA GTPase. 
    Immunity 35, 514 (2011) 
  • Jaenicke E, Büchler K, Decker H, Markl J, Barends T, and Schröder GF 
    The Refined Structure of Functional Unit h of Keyhole Limpet Hemocyanin (KLH1-h) Reveals Disulfide Bridges. 
    IUBMB Life 63(3), 183 (2011) 
  • Thielmann Y, Weiergräber OH, Mohrlüder J, Willbold D 
    Structural framework of the GABARAP-calreticulin interface - implications for substrate binding to endoplasmic reticulum chaperones 
    FEBS J 276, 1140-1152 (2009) 
  • Weiergräber OH, Stangler T, Thielmann Y, Mohrlüder J, Wiesehan K, Willbold D 
    Ligand binding mode of GABAA receptor-associated protein 
    J Mol Biol 381, 1320-1331 (2008)