Crystal structure of thermolysin delivered in polyacrylamide using x-ray free electron laser

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report

This is version 2.5 of the entry. See complete history


Polyacrylamide injection matrix for serial femtosecond crystallography.

Park, J.Park, S.Kim, J.Park, G.Cho, Y.Nam, K.H.

(2019) Sci Rep 9: 2525-2525

  • DOI: https://doi.org/10.1038/s41598-019-39020-9
  • Primary Citation of Related Structures:  
    6IG6, 6IG7

  • PubMed Abstract: 

    Serial femtosecond crystallography (SFX) provides opportunities to observe the dynamics of macromolecules without causing radiation damage at room temperature. Although SFX provides a biologically more reliable crystal structure than provided by the existing synchrotron sources, there are limitations due to the consumption of many crystal samples. A viscous medium as a carrier matrix reduces the flow rate of the crystal sample from the injector, thereby dramatically reducing sample consumption. However, the currently available media cannot be applied to specific crystal samples owing to reactions between the viscous medium and crystal sample. The discovery and characterisation of a new delivery medium for SFX can further expand its use. Herein, we report the preparation of a polyacrylamide (PAM) injection matrix to determine the crystal structure with an X-ray free-electron laser. We obtained 11,936 and 22,213 indexed images using 0.5 mg lysozyme and 1.0 mg thermolysin, respectively. We determined the crystal structures of lysozyme and thermolysin delivered in PAM at 1.7 Å and 1.8 Å resolutions. The maximum background scattering from PAM was lower than monoolein, a commonly used viscous medium. Our results show that PAM can be used as a sample delivery media in SFX studies.

  • Organizational Affiliation

    Pohang Accelerator Laboratory, Pohang, Gyeongbuk, Republic of Korea. jaehyun.park@postech.ac.kr.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thermolysin316Bacillus thermoproteolyticusMutation(s): 0 
Gene Names: npr
Find proteins for P00800 (Bacillus thermoproteolyticus)
Explore P00800 
Go to UniProtKB:  P00800
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00800
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on LYS

Download Ideal Coordinates CCD File 
H [auth A]LYSINE
C6 H15 N2 O2
Query on LEU

Download Ideal Coordinates CCD File 
C6 H13 N O2
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Query on CA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.663α = 90
b = 92.663β = 90
c = 128.591γ = 120
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: 2018-11-07 
  • Deposition Author(s): Nam, K.H.

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

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 2.0: 2019-01-23
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2019-05-22
    Changes: Data collection, Database references
  • Version 2.2: 2019-08-28
    Changes: Data collection
  • Version 2.3: 2019-09-18
    Changes: Data collection
  • Version 2.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations
  • Version 2.5: 2023-11-22
    Changes: Refinement description