1GWD

Tri-iodide derivative of hen egg-white lysozyme

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Triiodide Derivatization and Combinatorial Counter-Ion Replacement: Two Methods for Enhancing Phasing Signal Using Laboratory Cu Kalpha X-Ray Equipment

Evans, G., Bricogne, G.

(2002) Acta Crystallogr.,Sect.D 58: 976

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • A series of experiments performed at Cu Kalpha wavelength on in-house X-ray equipment are presented which investigate two possibilities for enhancing the experimental phasing signal by means of (i) triiodide/iodide soaks using KI/I(2) and (ii) combin ...

    A series of experiments performed at Cu Kalpha wavelength on in-house X-ray equipment are presented which investigate two possibilities for enhancing the experimental phasing signal by means of (i) triiodide/iodide soaks using KI/I(2) and (ii) combinations of counter-ions introduced using the short cryosoak method. Triiodide-derivative crystal structures for five test proteins have been refined and reveal that iodine can bind as polyiodide and single iodide ions through hydrophobic and hydrogen-bonding interactions both at the molecular surface and in intramolecular and intermolecular cavities. In three cases, the structures could be automatically determined with autoSHARP using in-house SAD and SIRAS data. The investigation of combinatorial counter-ion replacement using multiple salts with Na(+) and Cs(+) as cations and I(-) and Cl(-) as anions reveals that, for the case of hen egg-white lysozyme, significant improvement in phasing signal is obtained by the combined use of salts compared with SIRAS methods using native and single short-soak derivative data sets.

    Organizational Affiliation: 

    Global Phasing Limited, Cambridge, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME C
A
129Gallus gallusMutation(s): 0 
Gene 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 5 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
IOD
Query on IOD
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Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO
Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CMO
Query on CMO
Download SDF File 
Download CCD File 
A
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.168 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.050α = 90.00
b = 79.050β = 90.00
c = 36.820γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTER-TNTrefinement
MOSFLMdata reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-06-28
    Type: Data collection