6LAV

MicroED structure of lysozyme at 1.73A determained using crystal lamellas prepared by focused ion beam milling

  • Classification: HYDROLASE
  • Organism(s): Gallus gallus
  • Mutation(s): No 

  • Deposited: 2019-11-13 Released: 2019-11-27 
  • Deposition Author(s): Zhou, H., Luo, Z., Li, X.
  • Funding Organization(s): National Natural Science Foundation of China, Ministry of Science and Technology (China)

Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 1.73 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

wwPDB Validation 3D Report Full Report



Literature

Using focus ion beam to prepare crystal lamella for electron diffraction.

Zhou, H.Luo, Z.Li, X.

(2019) J Struct Biol 205: 59-64

  • DOI: 10.1016/j.jsb.2019.02.004
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Electron diffraction provides a powerful tool to solve the structures of small protein crystals. However, strong interactions between the electrons and the materials limit the application of the electron crystallographic method on large protein cryst ...

    Electron diffraction provides a powerful tool to solve the structures of small protein crystals. However, strong interactions between the electrons and the materials limit the application of the electron crystallographic method on large protein crystals with micrometer or larger sizes. Here, we used the focused ion beam (FIB) equipped on the scanning electron microscope (SEM) to mill a large crystal to thin lamella. The influences of the milling on the crystal lamella were observed and investigated, including radiation damage on the crystal surface during the FIB imaging, deformation of the thin crystal lamella, and variation in the diffraction intensities under electron radiation. These observations provide important information to optimize the FIB milling, and hence is important to obtain high-quality crystal samples for routine structure determination of protein crystals using the electron cryo-microscope.


    Organizational Affiliation

    Key Laboratory of Protein Sciences (Tsinghua University), Ministry of Education, Beijing, China; School of Life Sciences, Tsinghua University, Beijing, China. Electronic address: lixueming@mail.tsinghua.edu.cn.



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 UniProtKB:  P00698
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 1.73 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.986α = 90
b = 78.986β = 90
c = 37.889γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-11-13 
  • Released Date: 2019-11-27 
  • Deposition Author(s): Zhou, H., Luo, Z., Li, X.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31570730
National Natural Science Foundation of ChinaChina31722015
Ministry of Science and Technology (China)China2016YFA0501102
Ministry of Science and Technology (China)China2016YFA0501902

Revision History 

  • Version 1.0: 2019-11-27
    Type: Initial release