1LZ9

ANOMALOUS SIGNAL OF SOLVENT BROMINES USED FOR PHASING OF LYSOZYME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

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This is version 1.3 of the entry. See complete history


Literature

Anomalous signal of solvent bromides used for phasing of lysozyme.

Dauter, Z.Dauter, M.

(1999) J Mol Biol 289: 93-101

  • DOI: https://doi.org/10.1006/jmbi.1999.2744
  • Primary Citation of Related Structures:  
    1LZ9

  • PubMed Abstract: 

    The anomalous signal of bromide ions, present in the crystal structure of tetragonal hen egg-white lysozyme through the substitution of NaCl by NaBr in the crystallization medium, was used for phasing of X-ray data collected to 1.7 A resolution with a wavelength near the absorption edge of bromine. Phasing of a single wavelength data set, based purely on anomalous deltaf " contribution, led to easily interpretable electron density, equivalent to the complete multiwavelength anonalous dispersion phasing based on four-wavelength data. The classic small-structure direct methods program SHELXS run against all anomalous differences gave a successful solution of six highest peaks corresponding to six bromide ions in the structure with data limited up to a resolution of 3.5 A. Interpretable maps were obtained at a resolution up to 3.0 A using programs MLPHARE and DM. Bromide ions occupy well ordered positions at the protein surface. Phasing based on the single wavelength signal of anomalous scatterers introduced into the ordered solvent shell can be proposed as a tool for solving structures of well diffracting crystals.


  • Organizational Affiliation

    National Cancer Institute, Frederick and Brookhaven National Laboratory, NSLS, Building 725A-X9, Upton, NY, 11973, USA. dauter@bnl.gov


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (LYSOZYME)129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.6α = 90
b = 78.6β = 90
c = 37.2γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
REFMACrefinement
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-05-26
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Refinement description