9H4A | pdb_00009h4a

Ribonuclease-three Like 4 crystallization and structure determination at room temperature in the CrystalChip

• PDB DOI: https://doi.org/10.2210/pdb9H4A/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-18 Released: 2024-12-11 
• Deposition Author(s): Engilberge, S., Vincent, R., Coudray, L., Nilles, L., Scheer, H., Ritzenthaler, C., 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: 2.80 Å
• R-Value Free: 
  0.256 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.216 (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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 35.22 kDa 
• Atom Count: 2,131 
• Modeled Residue Count: 282 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein NUCLEAR FUSION DEFECTIVE 2	A, B	163	Arabidopsis thaliana	Mutation(s): 0  Gene Names: NFD2, At1g24450, F21J9.11
UniProt
Find proteins for Q9FYL8 (Arabidopsis thaliana) Explore Q9FYL8  Go to UniProtKB:  Q9FYL8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.256 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.13	α = 90
b = 101.53	β = 90
c = 134.03	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: 2024-12-11 
Deposition Author(s): Engilberge, S., Vincent, R., Coudray, L., Nilles, L., Scheer, H., Ritzenthaler, C., 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: 2024-12-11
  Type: Initial release
  
• Version 1.1: 2025-04-16
  Changes: Database references