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 

wwPDB Validation   3D Report Full Report


This is version 1.4 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

    Division of Structural Biology, Headington, Oxford, OX3 7BN, UK.


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