6H0L

Hen egg-white lysozyme structure determined with data from the EuXFEL, 9.22 keV photon energy


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Megahertz data collection from protein microcrystals at an X-ray free-electron laser.

Grunbein, M.L.Bielecki, J.Gorel, A.Stricker, M.Bean, R.Cammarata, M.Dorner, K.Frohlich, L.Hartmann, E.Hauf, S.Hilpert, M.Kim, Y.Kloos, M.Letrun, R.Messerschmidt, M.Mills, G.Nass Kovacs, G.Ramilli, M.Roome, C.M.Sato, T.Scholz, M.Sliwa, M.Sztuk-Dambietz, J.Weik, M.Weinhausen, B.Al-Qudami, N.Boukhelef, D.Brockhauser, S.Ehsan, W.Emons, M.Esenov, S.Fangohr, H.Kaukher, A.Kluyver, T.Lederer, M.Maia, L.Manetti, M.Michelat, T.Munnich, A.Pallas, F.Palmer, G.Previtali, G.Raab, N.Silenzi, A.Szuba, J.Venkatesan, S.Wrona, K.Zhu, J.Doak, R.B.Shoeman, R.L.Foucar, L.Colletier, J.P.Mancuso, A.P.Barends, T.R.M.Stan, C.A.Schlichting, I.

(2018) Nat Commun 9: 3487-3487

  • DOI: 10.1038/s41467-018-05953-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • X-ray free-electron lasers (XFELs) enable novel experiments because of their high peak brilliance and femtosecond pulse duration. However, non-superconducting XFELs offer repetition rates of only 10-120 Hz, placing significant demands on beam time an ...

    X-ray free-electron lasers (XFELs) enable novel experiments because of their high peak brilliance and femtosecond pulse duration. However, non-superconducting XFELs offer repetition rates of only 10-120 Hz, placing significant demands on beam time and sample consumption. We describe serial femtosecond crystallography experiments performed at the European XFEL, the first MHz repetition rate XFEL, delivering 1.128 MHz X-ray pulse trains at 10 Hz. Given the short spacing between pulses, damage caused by shock waves launched by one XFEL pulse on sample probed by subsequent pulses is a concern. To investigate this issue, we collected data from lysozyme microcrystals, exposed to a ~15 μm XFEL beam. Under these conditions, data quality is independent of whether the first or subsequent pulses of the train were used for data collection. We also analyzed a mixture of microcrystals of jack bean proteins, from which the structure of native, magnesium-containing concanavalin A was determined.


    Organizational Affiliation

    Department of Physics, UMR 625, UBL, University of Rennes 1, 35042, Rennes, France.,Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany.,Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany. Ilme.Schlichting@mpimf-heidelberg.mpg.de.,BioXFEL STC, 700 Ellicott Street, Buffalo, NY, 14203, USA.,Biological Research Centre (BRC), Hungarian Academy of Sciences, Temesvári krt. 62, Szeged, 6726, Hungary.,Center for Free-Electron Laser Science, Deutsches Elektronensynchrotron, Notkestraße 85, 22607, Hamburg, Germany.,Laboratoire de Spectrochimie Infrarouge et Raman, CNRS, UMR 8516, Université de Lille, 59000, Lille, France.,Deutsches Elektronensynchrotron DESY, Notkestraße 85, 22607, Hamburg, Germany.,Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany. Thomas.Barends@mpimf-heidelberg.mpg.de.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France.,ARC Centre of Excellence for Advanced Molecular Imaging, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.,European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.,Department of Physics, Rutgers University Newark, 101 Warren Street, Newark, NJ, 07102, USA. claudiu.stan@rutgers.edu.




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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.188 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 80.050α = 90.00
b = 80.050β = 90.00
c = 38.600γ = 90.00
Software Package:
Software NamePurpose
CrystFELdata scaling
PHENIXrefinement
CrystFELdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2018-09-12
    Type: Data collection, Database references
  • Version 1.2: 2018-11-14
    Type: Data collection