5GX1

Luciferin-regenerating enzyme collected with serial synchrotron rotational crystallography with accumulated dose of 1.1 MGy (1st measurement)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography

Hasegawa, K.Yamashita, K.Murai, T.Nuemket, N.Hirata, K.Ueno, G.Ago, H.Nakatsu, T.Kumasaka, T.Yamamoto, M.

(2017) J Synchrotron Radiat 24: 29-41

  • DOI: https://doi.org/10.1107/S1600577516016362
  • Primary Citation of Related Structures:  
    5GX1, 5GX2, 5GX3, 5GX4, 5GX5

  • PubMed Abstract: 

    Serial crystallography, in which single-shot diffraction images are collected, has great potential for protein microcrystallography. Although serial femtosecond crystallography (SFX) has been successfully demonstrated, limited beam time prevents its routine use. Inspired by SFX, serial synchrotron crystallography (SSX) has been investigated at synchrotron macromolecular crystallography beamlines. Unlike SFX, the longer exposure time of milliseconds to seconds commonly used in SSX causes radiation damage. However, in SSX, crystals can be rotated during the exposure, which can achieve efficient coverage of the reciprocal space. In this study, mercury single-wavelength anomalous diffraction (Hg-SAD) phasing of the luciferin regenerating enzyme (LRE) was performed using serial synchrotron rotation crystallography. The advantages of rotation and influence of dose on the data collected were evaluated. The results showed that sample rotation was effective for accurate data collection, and the optimum helical rotation step depended on multiple factors such as multiplicity and partiality of reflections, exposure time per rotation angle and the contribution from background scattering. For the LRE microcrystals, 0.25° was the best rotation step for the achievable resolution limit, whereas a rotation step larger than or equal to 1° was favorable for Hg-SAD phasing. Although an accumulated dose beyond 1.1 MGy caused specific damage at the Hg site, increases in resolution and anomalous signal were observed up to 3.4 MGy because of a higher signal-to-noise ratio.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Luciferin regenerating enzyme311Photinus pyralisMutation(s): 0 
UniProt
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.415α = 90
b = 76.724β = 90
c = 84.206γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata processing
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-04
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description