Structure of HYPER-VIL-lysozyme

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.252 

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New methods to prepare iodinated derivatives by vaporizing iodine labelling (VIL) and hydrogen peroxide VIL (HYPER-VIL)

Miyatake, H.Hasegawa, T.Yamano, A.

(2006) Acta Crystallogr D Biol Crystallogr 62: 280-289

  • DOI: https://doi.org/10.1107/S0907444905041909
  • Primary Citation of Related Structures:  
    2D8O, 2D8P, 2D8W, 2D91, 2D97, 2D98

  • PubMed Abstract: 

    New techniques are presented for the preparation of iodine derivatives, involving vapour diffusion of iodine. Firstly, in the vaporizing iodine labelling (VIL) technique, a small amount of KI/I(2) solution is enclosed in a crystallization well, with the result that gaseous I(2) molecules diffuse into the crystallization droplets without exerting substantial changes in ionic strength in the target crystals. Once they have diffused into the droplet, the I(2) molecules sometimes iodinate accessible tyrosines at ortho positions. Secondly, when iodination is insufficient, the hydrogen peroxide VIL (HYPER-VIL) technique can be further applied to increase the iodination ratio by the addition of a small droplet of hydrogen peroxide (H(2)O(2)) to the crystallization well; the gaseous H(2)O(2) also diffuses into the crystallization droplet to emphasize the iodination. These techniques are most effective for phase determination when coupled with softer X-rays, such as those from Cu Kalpha or Cr Kalpha radiation. The effectiveness of these techniques was assessed using five different crystals. Four of the crystals were successfully iodinated, providing sufficient phasing power for structure determination.

  • Organizational Affiliation

    RIKEN Harima Institute/SPring-8, Sayo-cho, Sayo-gun, Hyogo, Japan. miyatake@postman.riken.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus gallusMutation(s): 0 
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

  • Resolution: 2.10 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.252 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.692α = 90
b = 79.692β = 90
c = 36.118γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance