Experimental Data Snapshot

  • Resolution: 0.95 Å
  • R-Value Free: 0.147 
  • R-Value Observed: 0.114 

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This is version 1.3 of the entry. See complete history


Refinement of triclinic hen egg-white lysozyme at atomic resolution.

Walsh, M.A.Schneider, T.R.Sieker, L.C.Dauter, Z.Lamzin, V.S.Wilson, K.S.

(1998) Acta Crystallogr D Biol Crystallogr 54: 522-546

  • DOI: https://doi.org/10.1107/s0907444997013656
  • Primary Citation of Related Structures:  
    3LZT, 4LZT

  • PubMed Abstract: 

    X-ray diffraction data have been collected at both low (120 K) and room temperature from triclinic crystals of hen egg-white lysozyme to 0.925 and 0.950 A resolution, respectively, using synchrotron radiation. Data from one crystal were sufficient for the low-temperature study, whereas three crystals were required at room temperature. Refinement was carried out using the programs PROLSQ, ARP and SHELXL to give final conventional R factors of 8.98 and 10.48% for data with F > 4sigma(F) for the low- and room-temperature structures, respectively. The estimated r.m.s. coordinate error is 0.032 A for protein atoms, 0.050 A for all atoms in the low-temperature study, and 0.038 A for protein atoms and 0.049 A for all atoms in the room-temperature case, as estimated from inversion of the blocked least-squares matrix. The low-temperature study revealed that the side chains of 24 amino acids had multiple conformations. A total of 250 waters, six nitrate ions and three acetate ions, two of which were modelled with alternate orientations were located in the electron-density maps. Three sections of the main chain were modelled in alternate conformations. The room-temperature study produced a model with multiple conformations for eight side chains and a total of 139 water molecules, six nitrate but no acetate ions. The occupancies of the water molecules were refined in both structures and this step was shown to be meaningful when assessed by use of the free R factor. A detailed description and comparison of the structures is made with reference to the previously reported structure refined at 2.0 A resolution.

  • Organizational Affiliation

    European Molecular Biology Laboratory (EMBL), c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany. walsh@anl.gov

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LYSOZYME129Gallus 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: 0.95 Å
  • R-Value Free: 0.147 
  • R-Value Observed: 0.114 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.24α = 88.52
b = 31.87β = 108.53
c = 34.23γ = 111.89
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-96model building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-04-01
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description