6FTR | pdb_00006ftr

Serial Femtosecond Crystallography at Megahertz pulse rates

• PDB DOI: https://doi.org/10.2210/pdb6FTR/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2018-02-23 Released: 2018-10-10 
• Deposition Author(s): Wiedorn, M.O., Oberthuer, D., Barty, A., Chapman, H.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.173 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Megahertz serial crystallography.

Wiedorn, M.O., Oberthur, D., Bean, R., Schubert, R., Werner, N., Abbey, B., Aepfelbacher, M., Adriano, L., Allahgholi, A., Al-Qudami, N., Andreasson, J., Aplin, S., Awel, S., Ayyer, K., Bajt, S., Barak, I., Bari, S., Bielecki, J., Botha, S., Boukhelef, D., Brehm, W., Brockhauser, S., Cheviakov, I., Coleman, M.A., Cruz-Mazo, F., Danilevski, C., Darmanin, C., Doak, R.B., Domaracky, M., Dorner, K., Du, Y., Fangohr, H., Fleckenstein, H., Frank, M., Fromme, P., Ganan-Calvo, A.M., Gevorkov, Y., Giewekemeyer, K., Ginn, H.M., Graafsma, H., Graceffa, R., Greiffenberg, D., Gumprecht, L., Gottlicher, P., Hajdu, J., Hauf, S., Heymann, M., Holmes, S., Horke, D.A., Hunter, M.S., Imlau, S., Kaukher, A., Kim, Y., Klyuev, A., Knoska, J., Kobe, B., Kuhn, M., Kupitz, C., Kupper, J., Lahey-Rudolph, J.M., Laurus, T., Le Cong, K., Letrun, R., Xavier, P.L., Maia, L., Maia, F.R.N.C., Mariani, V., Messerschmidt, M., Metz, M., Mezza, D., Michelat, T., Mills, G., Monteiro, D.C.F., Morgan, A., Muhlig, K., Munke, A., Munnich, A., Nette, J., Nugent, K.A., Nuguid, T., Orville, A.M., Pandey, S., Pena, G., Villanueva-Perez, P., Poehlsen, J., Previtali, G., Redecke, L., Riekehr, W.M., Rohde, H., Round, A., Safenreiter, T., Sarrou, I., Sato, T., Schmidt, M., Schmitt, B., Schonherr, R., Schulz, J., Sellberg, J.A., Seibert, M.M., Seuring, C., Shelby, M.L., Shoeman, R.L., Sikorski, M., Silenzi, A., Stan, C.A., Shi, X., Stern, S., Sztuk-Dambietz, J., Szuba, J., Tolstikova, A., Trebbin, M., Trunk, U., Vagovic, P., Ve, T., Weinhausen, B., White, T.A., Wrona, K., Xu, C., Yefanov, O., Zatsepin, N., Zhang, J., Perbandt, M., Mancuso, A.P., Betzel, C., Chapman, H., Barty, A.

(2018) Nat Commun 9: 4025-4025

• PubMed: 30279492 
• DOI: https://doi.org/10.1038/s41467-018-06156-7
• Primary Citation Related Structures: 
  6FTR, 6GTH


• PubMed Abstract: 
  

  The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a β-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.

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Organizational Affiliation: 
• Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.
Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany.
Integrated Biology Infrastructure Life-Science Facility at the European XFEL (XBI), Holzkoppel 4, 22869, Schenefeld, Germany.
Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC, 3086, Australia.
Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany.
Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden.
ELI Beamlines, Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21, Prague, Czech Republic.
Condensed Matter Physics, Department of Physics, Chalmers University of Technology, Gothenburg, 412 96, Sweden.
Institute of Molecular Biology, SAS, Dubravska cesta 21, 845 51, Bratislava, Slovakia.
Biological Research Centre (BRC), Hungarian Academy of Sciences, Temesvári krt. 62, Szeged, 6726, Hungary.
Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA.
Depart. Ingeniería Aeroespacial y Mecánica de Fluidos ETSI, Universidad de Sevilla, 41092, Sevilla, Spain.
Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany.
Engineering and the Environment, University of Southampton, SO17 1BJ, Southampton, UK.
School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-1604, USA.
Hamburg University of Technology, Vision Systems E-2, Harburger Schloßstr. 20, 21079, Hamburg, Germany.
Division of Structural Biology, Headington, Oxford, OX3 7BN, UK.
Diamond Light Source, Research Complex at Harwell, and University of Oxford, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK.
Mid Sweden University, Holmgatan 10, 85170, Sundsvall, Sweden.
Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen, Switzerland.
Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany.
Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, 94025, CA, USA.
School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia.
Physics Department, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA.
Department of Chemistry, Universität Hamburg, Martin-Luther-King Platz 6, 20146, Hamburg, Germany.
Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.
Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany.
NERSC, Lawrence Berkeley National Laboratory, Berkeley, 94720, CA, USA.
Biomedical and X-Ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, Stockholm, 106 91, Sweden.
Physics Department, Rutgers University Newark, Newark, NJ, 07102, USA.
Department of Chemistry, University at Buffalo, 359 Natural Sciences Complex, Buffalo, NY, 14260, USA.
Institute of Nanostructure and Solid State Physics, Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
Institute for Glycomics, Griffith University, Southport, QLD, 4222, Australia.
Department of Physics, Arizona State University, Tempe, AZ, 85287, USA.
Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany. [e-mail].
Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany. [e-mail].
The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany. [e-mail].
Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.85 kDa 
• Atom Count: 1,248 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	E [auth A], F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.173 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Diffraction Data: https://doi.org/10.11577/1464102

Diffraction Data: https://doi.org/10.11577/1464101

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.3	α = 90
b = 79.3	β = 90
c = 37.73	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-10 
Deposition Author(s): Wiedorn, M.O., Oberthuer, D., Barty, A., Chapman, H.N.

Revision History  

• Version 1.0: 2018-10-10
  Type: Initial release
  
• Version 1.1: 2018-10-17
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references
• Version 1.4: 2024-01-17
  Changes: Refinement description
• Version 1.5: 2024-10-09
  Changes: Structure summary