7DTF

Room temperature structure of lysozyme by serial millisecond crystallography

• PDB DOI: https://doi.org/10.2210/pdb7DTF/pdb

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


• Deposited: 2021-01-04 Released: 2021-01-20 
• Deposition Author(s): Nam, K.H.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.256 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 

Starting Model: experimental

Literature

Room temperature structure of lysozyme by serial millisecond crystallography

Nam, K.H.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 16.35 kDa 
• Atom Count: 1,059 
• Modelled 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]	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: 1.85 Å
• R-Value Free: 0.256 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data: https://doi.org/10.11577/1844335

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.44	α = 90
b = 79.44	β = 90
c = 38.41	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystFEL	data reduction
CrystFEL	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-01-20 
Deposition Author(s): Nam, K.H.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2017M3A9F6029736

Revision History  

• Version 1.0: 2021-01-20
  Type: Initial release
  
• Version 1.1: 2023-09-06
  Changes: Data collection, Database references
• Version 1.2: 2023-11-29
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary