6JZI

Structure of hen egg-white lysozyme obtained from SFX experiments under atmospheric pressure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

High-viscosity sample-injection device for serial femtosecond crystallography at atmospheric pressure.

Shimazu, Y.Tono, K.Tanaka, T.Yamanaka, Y.Nakane, T.Mori, C.Terakado Kimura, K.Fujiwara, T.Sugahara, M.Tanaka, R.Doak, R.B.Shimamura, T.Iwata, S.Nango, E.Yabashi, M.

(2019) J Appl Crystallogr 52: 1280-1288

  • DOI: https://doi.org/10.1107/S1600576719012846
  • Primary Citation of Related Structures:  
    6JZH, 6JZI

  • PubMed Abstract: 

    A sample-injection device has been developed at SPring-8 Angstrom Compact Free-Electron Laser (SACLA) for serial femtosecond crystallography (SFX) at atmospheric pressure. Microcrystals embedded in a highly viscous carrier are stably delivered from a capillary nozzle with the aid of a coaxial gas flow and a suction device. The cartridge-type sample reservoir is easily replaceable and facilitates sample reloading or exchange. The reservoir is positioned in a cooling jacket with a temperature-regulated water flow, which is useful to prevent drastic changes in the sample temperature during data collection. This work demonstrates that the injector successfully worked in SFX of the human A 2A adenosine receptor complexed with an antagonist, ZM241385, in lipidic cubic phase and for hen egg-white lysozyme microcrystals in a grease carrier. The injection device has also been applied to many kinds of proteins, not only for static structural analyses but also for dynamics studies using pump-probe techniques.


  • Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan.


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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.11α = 90
b = 79.11β = 90
c = 38.02γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanBasis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)
Ministry of Education, Culture, Sports, Science and Technology (Japan)JapanX-ray Free-Electron Laser Priority Strategy Program

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-30
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2023-11-22
    Changes: Refinement description