Serial femtosecond X-ray structure of Agrocybe cylindracea galectin with lactose solved by Se-SAD using XFEL (refined against 60,000 patterns)

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.149 

wwPDB Validation   3D Report Full Report

This is version 3.3 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
Galactoside-binding lectin
A, B
178Agrocybe cylindraceaMutation(s): 0 
Find proteins for A0A2D0TCI3 (Agrocybe cylindracea)
Explore A0A2D0TCI3 
Go to UniProtKB:  A0A2D0TCI3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2D0TCI3
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
C, D
Glycosylation Resources
GlyTouCan:  G74303MH
GlyCosmos:  G74303MH
GlyGen:  G74303MH
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.795α = 90
b = 105.795β = 90
c = 75.46γ = 120
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: 2018-01-24
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.0: 2020-08-05
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2020-10-14
    Changes: Structure summary
  • Version 3.2: 2023-09-06
    Changes: Data collection, Database references
  • Version 3.3: 2023-11-15
    Changes: Data collection