6H3B

Lysozyme: Machining protein microcrystals for structure determination by electron diffraction

• PDB DOI: https://doi.org/10.2210/pdb6H3B/pdb

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


• Deposited: 2018-07-18 Released: 2018-09-12 
• Deposition Author(s): Duyvesteyn, H.M.E., Ginn, H.M., Stuart, D.I.
• Funding Organization(s): Medical Research Council (United Kingdom), Wellcome Trust, National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 1.90 Å
• R-Value Free: 0.283 
• R-Value Work: 0.291 

Literature

Machining protein microcrystals for structure determination by electron diffraction.

Duyvesteyn, H.M.E., Kotecha, A., Ginn, H.M., Hecksel, C.W., Beale, E.V., de Haas, F., Evans, G., Zhang, P., Chiu, W., Stuart, D.I.

(2018) Proc Natl Acad Sci U S A 115: 9569-9573

• PubMed: 30171169 
• DOI: https://doi.org/10.1073/pnas.1809978115
• Primary Citation of Related Structures:  
  6H3B


• PubMed Abstract: 
  

  We demonstrate that ion-beam milling of frozen, hydrated protein crystals to thin lamella preserves the crystal lattice to near-atomic resolution. This provides a vehicle for protein structure determination, bridging the crystal size gap between the nanometer scale of conventional electron diffraction and micron scale of synchrotron microfocus beamlines. The demonstration that atomic information can be retained suggests that milling could provide such detail on sections cut from vitrified cells.

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Organizational Affiliation: 

Division of Structural Biology, University of Oxford, Headington, Oxford OX3 7BN, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 14.37 kDa 
• Atom Count: 1,016 
• Modelled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 1.90 Å
• R-Value Free: 0.283 
• R-Value Work: 0.291 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.9	α = 90
b = 79.9	β = 90
c = 38.67	γ = 90

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-09-12 
Deposition Author(s): Duyvesteyn, H.M.E., Ginn, H.M., Stuart, D.I.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MR/N00065X/1
Wellcome Trust	United Kingdom	ALR00750-B500.1
Wellcome Trust	United Kingdom	ALR00040
Wellcome Trust	United Kingdom	206422/Z/17/Z
Wellcome Trust	United Kingdom	101122/Z/13/Z
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	P41GM103832
Wellcome Trust	United Kingdom	090532/Z/09/Z

Revision History  

• Version 1.0: 2018-09-12
  Type: Initial release
  
• Version 1.1: 2018-09-26
  Changes: Data collection, Database references
• Version 1.2: 2022-03-30
  Changes: Author supporting evidence, Database references
• Version 1.3: 2024-11-13
  Changes: Data collection, Structure summary