Crystal structure of lysozyme by fixed-target serial femtosecond crystallography

  • Classification: HYDROLASE
  • Organism(s): Gallus gallus
  • Expression System: Gallus gallus
  • Mutation(s): No 

  • Deposited: 2018-11-13 Released: 2019-05-22 
  • Deposition Author(s): Nam, K.H.
  • Funding Organization(s): National Research Foundation (Korea)

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


Nylon mesh-based sample holder for fixed-target serial femtosecond crystallography.

Lee, D.Baek, S.Park, J.Lee, K.Kim, J.Lee, S.J.Chung, W.K.Lee, J.L.Cho, Y.Nam, K.H.

(2019) Sci Rep 9: 6971-6971

  • DOI: https://doi.org/10.1038/s41598-019-43485-z
  • Primary Citation of Related Structures:  
    6IRJ, 6IRK

  • PubMed Abstract: 

    Fixed-target serial femtosecond crystallography (FT-SFX) was an important advance in crystallography by dramatically reducing sample consumption, while maintaining the benefits of SFX for obtaining crystal structures at room temperature without radiation damage. Despite a number of advantages, preparation of a sample holder for the sample delivery in FT-SFX with the use of many crystals in a single mount at ambient temperature is challenging as it can be complicated and costly, and thus, development of an efficient sample holder is essential. In this study, we introduced a nylon mesh-based sample holder enclosed by a polyimide film. This sample holder can be rapidly manufactured using a commercially available nylon mesh with pores of a desired size at a low cost without challenging technology. Furthermore, this simple device is highly efficient in data acquisition. We performed FT-SFX using a nylon mesh-based sample holder and collected over 130,000 images on a single sample holder using a 30 Hz X-ray pulse for 1.2 h. We determined the crystal structures of lysozyme and glucose isomerase using the nylon mesh at 1.65 and 1.75 Å, respectively. The nylon mesh exposed to X-rays produced very low levels of background scattering at 3.75 and 4.30 Å, which are negligible for data analysis. Our method provides a simple and rapid but highly efficient way to deliver samples for FT-SFX.

  • Organizational Affiliation

    Department of Mechanical Engineering, POSTECH, Pohang, 37673, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus gallusMutation(s): 0 
Gene Names: LYZ
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.22α = 90
b = 78.22β = 90
c = 37.76γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

  • Released Date: 2019-05-22 
  • Deposition Author(s): Nam, K.H.

Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic OfNRF-2017M3A9F6029736
National Research Foundation (Korea)Korea, Republic OfNRF-2017R1D1A1B03033087

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection
  • Version 1.2: 2019-08-28
    Changes: Data collection
  • Version 1.3: 2019-09-18
    Changes: Data collection
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations
  • Version 1.5: 2023-11-22
    Changes: Refinement description