6FTR

Serial Femtosecond Crystallography at Megahertz pulse rates


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1038/s41467-018-06156-7
  • Primary Citation of Related Structures:  

  • 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 be ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.155 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.300α = 90.00
b = 79.300β = 90.00
c = 37.730γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata scaling
PHASERphasing
CrystFELdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2018-10-17
    Type: Data collection, Database references, Structure summary
  • Version 1.2: 2018-11-14
    Type: Data collection, Structure summary