3WXT

Crystal structure of hen egg-white lysozyme

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Grease matrix as a versatile carrier of proteins for serial crystallography

Sugahara, M., Mizohata, E., Nango, E., Suzuki, M., Tanaka, T., Masuda, T., Tanaka, R., Shimamura, T., Tanaka, Y., Suno, C., Ihara, K., Pan, D., Kakinouchi, K., Sugiyama, S., Murata, M., Inoue, T., Tono, K., Song, C., Park, J., Kameshima, T., Hatsui, T., Joti, Y., Yabashi, M., Iwata, S.

(2015) Nat Methods 12: 61-63

  • DOI: 10.1038/nmeth.3172
  • Primary Citation of Related Structures:  
    3WUL, 3WUM, 3WXQ, 3WXS, 3WXT, 3WXU, 4W4Q

  • PubMed Abstract: 

    • Serial femtosecond X-ray crystallography (SFX) has revolutionized atomic-resolution structural investigation by expanding applicability to micrometer-sized protein crystals, even at room temperature, and by enabling dynamics studies. However, reliable crystal-carrying media for SFX are lacking ...

    Serial femtosecond X-ray crystallography (SFX) has revolutionized atomic-resolution structural investigation by expanding applicability to micrometer-sized protein crystals, even at room temperature, and by enabling dynamics studies. However, reliable crystal-carrying media for SFX are lacking. Here we introduce a grease-matrix carrier for protein microcrystals and obtain the structures of lysozyme, glucose isomerase, thaumatin and fatty acid-binding protein type 3 under ambient conditions at a resolution of or finer than 2 Å.

    Organizational Affiliation: 

    1] RIKEN SPring-8 Center, Sayo, Japan. [2] Department of Cell Biology, Graduate School of Medicine, Kyoto University, Sakyo, Japan.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysozyme CA129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL
Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
B [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79α = 90
b = 79β = 90
c = 38γ = 90
Software Package:
Software NamePurpose
CrystFELdata collection
REFMACrefinement
CrystFELdata reduction
XDSdata scaling
REFMACphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2015-02-04
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Data collection, Refinement description