3J6K

2.5A structure of lysozyme solved by MicroED

• PDB DOI:  https://doi.org/10.2210/pdb3J6K/pdb
• EM Map EMD-6313: EMDB EMDataResource

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


• Deposited: 2014-03-18 Released: 2014-08-13 
• Deposition Author(s): Nannenga, B.L., Shi, D., Leslie, A.G.W., Gonen, T.

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 2.50 Å
• R-Value Free: 0.255 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 

Literature

High-resolution structure determination by continuous-rotation data collection in MicroED.

Nannenga, B.L., Shi, D., Leslie, A.G., Gonen, T.

(2014) Nat Methods 11: 927-930

• PubMed: 25086503 
• DOI: https://doi.org/10.1038/nmeth.3043
• Primary Citation of Related Structures:  
  3J6K, 5A3E


• PubMed Abstract: 
  

  MicroED uses very small three-dimensional protein crystals and electron diffraction for structure determination. We present an improved data collection protocol for MicroED called 'continuous rotation'. Microcrystals are continuously rotated during data collection, yielding more accurate data. The method enables data processing with the crystallographic software tool MOSFLM, which resulted in improved resolution for the model protein lysozyme. These improvements are paving the way for the broad implementation and application of MicroED in structural biology.

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Organizational Affiliation: 

Janelia Research Campus, Howard Hughes Medical Institute, Ashburn VA, USA.

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: 14.33 kDa 
• Atom Count: 1,024 
• 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  Gene Names: LYZ EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Experimental Data & Validation

Experimental Data

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 2.50 Å
• R-Value Free: 0.255 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data: https://doi.org/10.15785/SBGRID/185
• Diffraction Data: https://doi.org/10.15785/SBGRID/222

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.962	α = 90
b = 75.962	β = 90
c = 37.218	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-13 
Deposition Author(s): Nannenga, B.L., Shi, D., Leslie, A.G.W., Gonen, T.

Revision History  

• Version 1.0: 2014-08-13
  Type: Initial release
  
• Version 1.1: 2014-08-20
  Changes: Database references
• Version 1.2: 2014-09-10
  Changes: Database references
• Version 1.3: 2015-04-08
  Changes: Other