Millisecond cryo-trapping by the spitrobot crystal plunger, CTXM-14 Avibactam complex, SSX, 1 sec

Experimental Data Snapshot

  • Resolution: 1.97 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Millisecond cryo-trapping by the spitrobot crystal plunger simplifies time-resolved crystallography.

Mehrabi, P.Sung, S.von Stetten, D.Prester, A.Hatton, C.E.Kleine-Dopke, S.Berkes, A.Gore, G.Leimkohl, J.P.Schikora, H.Kollewe, M.Rohde, H.Wilmanns, M.Tellkamp, F.Schulz, E.C.

(2023) Nat Commun 14: 2365-2365

  • DOI: https://doi.org/10.1038/s41467-023-37834-w
  • Primary Citation of Related Structures:  
    8AW8, 8AW9, 8AWB, 8AWC, 8AWD, 8AWE, 8AWF, 8AWS, 8AWU, 8AWV, 8AWX, 8AWY, 8B03, 8B05, 8B06, 8B08, 8B2O, 8B2V, 8B2W, 8B3M

  • PubMed Abstract: 

    We introduce the spitrobot, a protein crystal plunger, enabling reaction quenching via cryo-trapping with a time-resolution in the millisecond range. Protein crystals are mounted on canonical micromeshes on an electropneumatic piston, where the crystals are kept in a humidity and temperature-controlled environment, then reactions are initiated via the liquid application method (LAMA) and plunging into liquid nitrogen is initiated after an electronically set delay time to cryo-trap intermediate states. High-magnification images are automatically recorded before and after droplet deposition, prior to plunging. The SPINE-standard sample holder is directly plunged into a storage puck, enabling compatibility with high-throughput infrastructure. Here we demonstrate binding of glucose and 2,3-butanediol in microcrystals of xylose isomerase, and of avibactam and ampicillin in microcrystals of the extended spectrum beta-lactamase CTX-M-14. We also trap reaction intermediates and conformational changes in macroscopic crystals of tryptophan synthase to demonstrate that the spitrobot enables insight into catalytic events.

  • Organizational Affiliation

    Institute for Nanostructure and Solid-State Physics, Universität Hamburg, Hamburg, Germany. pedram.mehrabi@uni-hamburg.de.

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
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NXL (Subject of Investigation/LOI)
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
Experimental Data & Validation

Experimental Data

  • Resolution: 1.97 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.85α = 90
b = 41.85β = 90
c = 232.85γ = 120
Software Package:
Software NamePurpose
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description