6WEC

Multi-Hit SFX using MHz XFEL sources


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.254 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers.

Holmes, S.Kirkwood, H.J.Bean, R.Giewekemeyer, K.Martin, A.V.Hadian-Jazi, M.Wiedorn, M.O.Oberthur, D.Marman, H.Adriano, L.Al-Qudami, N.Bajt, S.Barak, I.Bari, S.Bielecki, J.Brockhauser, S.Coleman, M.A.Cruz-Mazo, F.Danilevski, C.Dorner, K.Ganan-Calvo, A.M.Graceffa, R.Fanghor, H.Heymann, M.Frank, M.Kaukher, A.Kim, Y.Kobe, B.Knoska, J.Laurus, T.Letrun, R.Maia, L.Messerschmidt, M.Metz, M.Michelat, T.Mills, G.Molodtsov, S.Monteiro, D.C.F.Morgan, A.J.Munnich, A.Pena Murillo, G.E.Previtali, G.Round, A.Sato, T.Schubert, R.Schulz, J.Shelby, M.Seuring, C.Sellberg, J.A.Sikorski, M.Silenzi, A.Stern, S.Sztuk-Dambietz, J.Szuba, J.Trebbin, M.Vagovic, P.Ve, T.Weinhausen, B.Wrona, K.Xavier, P.L.Xu, C.Yefanov, O.Nugent, K.A.Chapman, H.N.Mancuso, A.P.Barty, A.Abbey, B.Darmanin, C.

(2022) Nat Commun 13: 4708-4708

  • DOI: https://doi.org/10.1038/s41467-022-32434-6
  • Primary Citation of Related Structures:  
    6WEB, 6WEC, 7TUM

  • PubMed Abstract: 

    The European X-ray Free Electron Laser (XFEL) and Linac Coherent Light Source (LCLS) II are extremely intense sources of X-rays capable of generating Serial Femtosecond Crystallography (SFX) data at megahertz (MHz) repetition rates. Previous work has shown that it is possible to use consecutive X-ray pulses to collect diffraction patterns from individual crystals. Here, we exploit the MHz pulse structure of the European XFEL to obtain two complete datasets from the same lysozyme crystal, first hit and the second hit, before it exits the beam. The two datasets, separated by <1 µs, yield up to 2.1 Å resolution structures. Comparisons between the two structures reveal no indications of radiation damage or significant changes within the active site, consistent with the calculated dose estimates. This demonstrates MHz SFX can be used as a tool for tracking sub-microsecond structural changes in individual single crystals, a technique we refer to as multi-hit SFX.


  • Organizational Affiliation

    Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth A],
M [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.254 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.3α = 90
b = 79.3β = 90
c = 37.73γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Cheetahdata collection
Cootmodel building
CrystFELdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaCE140100011

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release
  • Version 1.1: 2022-11-02
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description