6GW9

Concanavalin A structure determined with data from the EuXFEL, the first MHz free electron laser


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1038/s41467-018-05953-4
  • Primary Citation of Related Structures:  
    6GW9, 6GWA, 6H0K, 6H0L

  • 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 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

    Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Concanavalin V237Canavalia catharticaMutation(s): 0 
UniProt
Find proteins for C0HJY1 (Canavalia cathartica)
Explore C0HJY1 
Go to UniProtKB:  C0HJY1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC0HJY1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.8α = 90
b = 88.1β = 90
c = 90.2γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2018-09-12
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-14
    Changes: Data collection
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description