Luciferin-regenerating enzyme solved by SAD using XFEL (refined against 11,000 patterns)

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography

Yamashita, K.Kuwabara, N.Nakane, T.Murai, T.Mizohata, E.Sugahara, M.Pan, D.Masuda, T.Suzuki, M.Sato, T.Kodan, A.Yamaguchi, T.Nango, E.Tanaka, T.Tono, K.Joti, Y.Kameshima, T.Hatsui, T.Yabashi, M.Manya, H.Endo, T.Kato, R.Senda, T.Kato, H.Iwata, S.Ago, H.Yamamoto, M.Yumoto, F.Nakatsu, T.

(2017) IUCrJ 4: 639-647

  • DOI: https://doi.org/10.1107/S2052252517008557
  • Primary Citation of Related Structures:  
    5XFC, 5XFD, 5XFE

  • PubMed Abstract: 

    Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) holds enormous potential for the structure determination of proteins for which it is difficult to produce large and high-quality crystals. SFX has been applied to various systems, but rarely to proteins that have previously unknown structures. Consequently, the majority of previously obtained SFX structures have been solved by the molecular replacement method. To facilitate protein structure determination by SFX, it is essential to establish phasing methods that work efficiently for SFX. Here, selenomethionine derivatization and mercury soaking have been investigated for SFX experiments using the high-energy XFEL at the SPring-8 Angstrom Compact Free-Electron Laser (SACLA), Hyogo, Japan. Three successful cases are reported of single-wavelength anomalous diffraction (SAD) phasing using X-rays of less than 1 Å wavelength with reasonable numbers of diffraction patterns (13 000, 60 000 and 11 000). It is demonstrated that the combination of high-energy X-rays from an XFEL and commonly used heavy-atom incorporation techniques will enable routine de novo structural determination of biomacromolecules.

  • Organizational Affiliation

    RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Luciferin regenerating enzyme311Photinus pyralisMutation(s): 0 
Find proteins for Q95YI4 (Photinus pyralis)
Explore Q95YI4 
Go to UniProtKB:  Q95YI4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ95YI4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.9α = 90
b = 77.03β = 90
c = 84.53γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-10-25
    Changes: Data collection, Database references
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations