8RPM

Lysozyme structure based on automated real-time serial crystallography data processing using CrystFEL

• PDB DOI: https://doi.org/10.2210/pdb8RPM/pdb

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


• Deposited: 2024-01-16 Released: 2024-02-21 
• Deposition Author(s): White, T.A., Oberthuer, D., Henkel, A.
• Funding Organization(s): H2020 Marie Curie Actions of the European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.222 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

Real-time data processing for serial crystallography experiments

White, T.A., Oberthuer, D., Henkel, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.43 kDa 
• Atom Count: 1,075 
• 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	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	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.222 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.2	α = 90
b = 79.2	β = 90
c = 38	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
PDB-REDO	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-21 
Deposition Author(s): White, T.A., Oberthuer, D., Henkel, A.

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Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	85764

Revision History  

• Version 1.0: 2024-02-21
  Type: Initial release