9H3E | pdb_00009h3e

Hen egg white lysozyme crystallization and structure determination at room temperature in the CrystalChip

• PDB DOI: https://doi.org/10.2210/pdb9H3E/pdb

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


• Deposited: 2024-10-16 Released: 2024-12-04 
• Deposition Author(s): Pachl, P., Coudray, L., VIncent, R., Sauter, C.
• Funding Organization(s): Centre National de la Recherche Scientifique (CNRS), Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.177 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.138 (DCC) 
• R-Value Observed: 
  0.140 (Depositor) 

Starting Model: experimental

Literature

Protein crystallization and structure determination at room temperature in the CrystalChip.

Pachl, P., Coudray, L., Vincent, R., Nilles, L., Scheer, H., Ritzenthaler, C., Fejfarova, A., Rezacova, P., Engilberge, S., Sauter, C.

(2025) FEBS Open Bio 15: 532-541

• PubMed: 39572886 
• DOI: https://doi.org/10.1002/2211-5463.13932
• Primary Citation of Related Structures:  
  9H3E, 9H3H, 9H4A


• PubMed Abstract: 
  

  The production of high-quality crystals is a key step in crystallography in general, but control of crystallization conditions is even more crucial in serial crystallography, which requires sets of crystals homogeneous in size and diffraction properties. This protocol describes the implementation of a simple and user-friendly microfluidic device that allows both the production of crystals by the counter-diffusion method and their in situ analysis by serial crystallography. As an illustration, the whole procedure is used to determine the crystal structure of three proteins from data collected at room temperature at a synchrotron radiation source.

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Organizational Affiliation: 
• CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, France.
Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Praha 6, Czech Republic.
CNRS, Institut de Biologie Moléculaire et Cellulaire, UPR 2357, Université de Strasbourg, France.
CNRS, CEA, Institut de Biologie Structurale (IBS), Université Grenoble Alpes, France.

Biological Assembly 1  

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

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

Biological Assembly Evidence: SAXS, gel filtration

Macromolecule Content 

• Total Structure Weight: 16.39 kDa 
• Atom Count: 1,103 
• Modeled Residue Count: 129 
• Deposited Residue Count: 147 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	147	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.177 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.138 (DCC) 
• R-Value Observed: 0.140 (Depositor) 

Diffraction Data: https://doi.org/10.15151/ESRF-ES-1752158517

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.16	α = 90
b = 79.16	β = 90
c = 38.15	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): Pachl, P., Coudray, L., VIncent, R., Sauter, C.

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Funding Organization	Location	Grant Number
Centre National de la Recherche Scientifique (CNRS)	France	--
Agence Nationale de la Recherche (ANR)	France	ANR-10-LABX-0036_NETRNA

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release
  
• Version 1.1: 2025-04-16
  Changes: Database references