9P6R | pdb_00009p6r

Structure of lysozyme-N,N',N"-triacetylchitotriose complex determined using REyes for automated MicroED

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

  • Deposited: 2025-06-19 Released: 2025-12-10 
  • Deposition Author(s): Eremin, D., Vlahakis, N.W., Rodriguez, J.A., Nelson, H.M.
  • Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Science Foundation (NSF, United States), National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)

Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.276 (Depositor), 0.303 (DCC) 
  • R-Value Work: 
    0.238 (Depositor), 0.254 (DCC) 
  • R-Value Observed: 
    0.242 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Spatially Aware Diffraction Mapping Enables Fully Autonomous MicroED.

Eremin, D.B.Jha, K.K.Delgadillo, D.A.Zhang, H.Foxman, S.H.Johnson, S.N.Vlahakis, N.W.Cascio, D.Lavallo, V.Rodriguez, J.A.Nelson, H.M.

(2025) J Am Chem Soc 147: 42299-42310

  • DOI: https://doi.org/10.1021/jacs.5c10751
  • Primary Citation of Related Structures:  
    9P6R

  • PubMed Abstract: 

    In the hands of experts, microcrystal electron diffraction (microED, a 3D ED method) is a powerful tool for structural chemistry and chemical discovery. To expand the accessibility and utility of microED, we introduce Reciprocal Eyes (REyes), an autonomous and intelligent platform (available for academic use) that combines diffraction-based particle selection with real-time data processing to deliver crystal structures without human intervention. REyes spatially maps diffraction signal and autonomously selects crystallites of interest, relying on lattice-quality metrics to acquire and index high-resolution data sets from diverse compounds. Tested on four different transmission electron microscopes (TEMs), it consistently yields preliminary ab initio structural solutions from single crystallites of materials, peptides, metal complexes, natural products (NPs), and proteins.


  • Organizational Affiliation
    • Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus gallusMutation(s): 0 
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
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth E]3N/A
Glycosylation Resources
GlyTouCan:  G47362BJ
GlyCosmos:  G47362BJ
GlyGen:  G47362BJ
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 2.20 Å
  • R-Value Free:  0.276 (Depositor), 0.303 (DCC) 
  • R-Value Work:  0.238 (Depositor), 0.254 (DCC) 
  • R-Value Observed: 0.242 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.57α = 90
b = 79.57β = 90
c = 39.83γ = 90
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United StatesHHMI-EPI
National Science Foundation (NSF, United States)United StatesCHE-1925607
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)United StatesR01AT011990
National Science Foundation (NSF, United States)United StatesDMR-1933487
National Science Foundation (NSF, United States)United StatesCHE-2003418

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release