1LZ9

ANOMALOUS SIGNAL OF SOLVENT BROMINES USED FOR PHASING OF LYSOZYME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1006/jmbi.1999.2744
  • Also Cited By: 1HF4

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (LYSOZYME)
A
129Gallus gallusGene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR

Download SDF File 
Download CCD File 
A
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.210 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.600α = 90.00
b = 78.600β = 90.00
c = 37.200γ = 90.00
Software Package:
Software NamePurpose
CCP4model building
CCP4phasing
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1999-03-15 
  • Released Date: 1999-05-26 
  • Deposition Author(s): Dauter, Z., Dauter, M.

Revision History 

  • Version 1.0: 1999-05-26
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance