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 
  • R-Value Observed: 0.157 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 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: https://doi.org/10.1038/s41467-018-06156-7
  • Primary Citation of 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.


  • Organizational Affiliation

    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus 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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
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
Query on ACT

Download Ideal Coordinates CCD File 
E [auth A],
F [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]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.3α = 90
b = 79.3β = 90
c = 37.73γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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