4YOP

CRYSTAL STRUCTURE OF HEN EGG-WHITE LYSOZYME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Native sulfur/chlorine SAD phasing for serial femtosecond crystallography

Nakane, T.Song, C.Suzuki, M.Nango, E.Kobayashi, J.Masuda, T.Inoue, S.Mizohata, E.Nakatsu, T.Tanaka, T.Tanaka, R.Shimamura, T.Tono, K.Joti, Y.Kameshima, T.Hatsui, T.Yabashi, M.Nureki, O.Iwata, S.Sugahara, M.

(2015) Acta Crystallogr.,Sect.D 71: 2519-2525

  • DOI: 10.1107/S139900471501857X

  • PubMed Abstract: 
  • Serial femtosecond crystallography (SFX) allows structures to be determined with minimal radiation damage. However, phasing native crystals in SFX is not very common. Here, the structure determination of native lysozyme from single-wavelength anomalo ...

    Serial femtosecond crystallography (SFX) allows structures to be determined with minimal radiation damage. However, phasing native crystals in SFX is not very common. Here, the structure determination of native lysozyme from single-wavelength anomalous diffraction (SAD) by utilizing the anomalous signal of sulfur and chlorine at a wavelength of 1.77 Å is successfully demonstrated. This sulfur SAD method can be applied to a wide range of proteins, which will improve the determination of native crystal structures.


    Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
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
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.157 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.200α = 90.00
b = 79.200β = 90.00
c = 37.900γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SHELXDEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Data collection, Derived calculations