Crystal structure of hen egg white lysozyme

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

Starting Model: experimental
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The reproducible normality of the crystallographic B-factor.

Ramos, N.G.Sarmanho, G.F.de Sa Ribeiro, F.de Souza, V.Lima, L.M.T.R.

(2022) Anal Biochem 645: 114594-114594

  • DOI: https://doi.org/10.1016/j.ab.2022.114594
  • Primary Citation of Related Structures:  
    7S27, 7S28, 7S29, 7S2A, 7S2B, 7S2C, 7S2D, 7S2E, 7S2F, 7S2G, 7S2Q, 7S2U, 7S2V, 7S2W, 7S30, 7S31, 7S32, 7S33, 7S34, 7S35

  • PubMed Abstract: 

    Reproducibility determines the utility of a measurement. In structural biology the reproducibility permeate areas such as mechanics, data measurement, data analysis and refinement. In order to access the reproducibility of the combined contribution of these sources in uncertainties of protein crystallography we evaluated four groups of parameters from data collection to final structural model. We used lysozyme as a model, with 20 datasets collected at 1.6 Å resolution using two dissimilar x-ray diffraction setups and refined through a single automatic pipeline without arbitrary interpretation. Besides statistical differences in some structural parameters, the reproducibility of the final refined models allowed the determination of positional uncertainty, in good agreement with the Luzzati coordinate error. While the raw B-factor was found non-reproducible, an empirical scaling/normalization resulted in reproducible B-factors. The validity of this empirical scaling was corroborated by the reproducibility of normalized B-factors of independently solved datasets from proteins (insulin and myoglobin) from varying space groups available from structural database. The reproducibility of normalized B-factor may reposition this displacement parameter in the analysis of chemical (ligands, pH) and physical (pressure, temperature, space groups) variables.

  • Organizational Affiliation

    National Institute for Metrology, Quality and Technology (INMETRO), INMETRO, Duque de Caxias, RJ, 25250-020, Brazil. Electronic address: nataliag.ramos@gmail.com.

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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.235α = 90
b = 78.235β = 90
c = 36.956γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SAINTdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description