9UYR | pdb_00009uyr

In situ structure of egg-white lysozyme using a goniometer-compatible chip-based platform

• PDB DOI: https://doi.org/10.2210/pdb9UYR/pdb

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


• Deposited: 2025-05-15 Released: 2026-03-25 
• Deposition Author(s): Ghosh, S.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 
  0.194 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

A user-friendly goniometer-compatible fixed-target platform for macromolecular crystallography at synchrotrons.

Ghosh, S., Banacore, A., Norder, P., Bjelcic, M., Kabbinale, A., Nileshwar, P., Wehlander, G., de Sanctis, D., Basu, S., Orlans, J., Vallejos, A., Chavas, L.M.G., Neutze, R., Branden, G.

(2026) J Appl Crystallogr 59: 303-315

• PubMed: 41959872 
• DOI: https://doi.org/10.1107/S1600576725011513
• Primary Citation Related Structures: 
  9S39, 9TBL, 9UYR, 9VDJ, 9VDX


• PubMed Abstract: 
  

  Fixed-target platforms provide convenient support for microcrystals during serial X-ray crystallography studies using synchrotron radiation. Here, we describe a simple user-friendly 3D-printed support where the crystals are sandwiched between two layers of thin X-ray-transparent membrane resulting in very low scattering background. The platform is compatible with magnetic mounting onto the standard goniometer of macromolecular crystallography beamlines. Our design utilizes a 96-well frame that facilitates hanging-drop experiments directly on the membrane using conventional crystallization plates, thereby eliminating multiple pipetting and crystal handling steps. Crystals can be enclosed in a sandwich and packed into 'cassettes', preventing the risk of the sample drying out during room-temperature transportation to synchrotron sources. The versatility of the platform is demonstrated by five structures solved using different crystallization and data-collection strategies. Lysozyme single-crystal rotational crystallography at room temperature is shown, as well as microcrystal serial data collection under cryogenic conditions. On-chip microcrystallization is illustrated by use of a photosynthetic reaction center as an example. Finally, serial crystallography data collection at room temperature from microcrystals of the membrane protein cytochrome c oxidase crystallized in lipidic cubic phase is presented.

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Organizational Affiliation: 
• Department of Chemistry and Molecular Biology Gothenburg University Sweden.
Department of Applied Physics, Graduate School of Engineering Nagoya University Japan.
BioMAX Beamline, MAX IV Laboratory Lund University Sweden.
European Synchrotron Radiation Facility Grenoble France.
European Molecular Biology Laboratory, Grenoble, France.
Nagoya University Synchrotron Radiation Research Center Nagoya University Japan.

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: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 14.39 kDa 
• Atom Count: 1,059 
• Modeled 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL (Subject of Investigation/LOI)	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA (Subject of Investigation/LOI)	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.194 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.116	α = 90
b = 79.116	β = 90
c = 37.925	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
autoPROC	data processing
PHENIX	phasing
PHENIX	refinement
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-03-25 
Deposition Author(s): Ghosh, S.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	--

Revision History  

• Version 1.0: 2026-03-25
  Type: Initial release
  
• Version 1.1: 2026-04-22
  Changes: Database references