6GTH

Serial Femtosecond Crystallography at Megahertz pulse rates


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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

    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
Beta-lactamase260Klebsiella pneumoniaeMutation(s): 0 
Gene Names: ctx-m-14
EC: 3.5.2.6
UniProt
Find proteins for A0A0H3H219 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286))
Explore A0A0H3H219 
Go to UniProtKB:  A0A0H3H219
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3H219
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NXL
Query on NXL

Download Ideal Coordinates CCD File 
B [auth A](2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide
C7 H13 N3 O6 S
WJDGWXPPFHLLNL-RITPCOANSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.84α = 90
b = 41.84β = 90
c = 233.28γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
Cheetahdata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyCluster of Excellence 1074

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
  • Version 1.2: 2018-11-14
    Changes: Data collection, Structure summary
  • Version 1.3: 2023-12-13
    Changes: Advisory, Data collection, Database references, Structure summary
  • Version 1.4: 2024-01-17
    Changes: Refinement description