6KD1 | pdb_00006kd1

Room temperature structure of lysozyme delivered in agarose by serial millisecond crystallography

• PDB DOI: https://doi.org/10.2210/pdb6KD1/pdb

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


• Deposited: 2019-06-30 Released: 2019-07-17 
• Deposition Author(s): Nam, K.H.
• Funding Organization(s): National Research Foundation (Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.224 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Stable sample delivery in viscous media via a capillary for serial crystallography.

Nam, K.H.

(2020) J Appl Crystallogr 53: 45-50

• DOI: https://doi.org/10.1107/S1600576719014985

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 16.35 kDa 
• Atom Count: 1,076 
• 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  Gene Names: LYZ 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:  0.224 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.74	α = 90
b = 79.74	β = 90
c = 38.56	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: 2019-07-17 
Deposition Author(s): Nam, K.H.

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

Revision History  

• Version 1.0: 2019-07-17
  Type: Initial release
  
• Version 1.1: 2019-08-28
  Changes: Data collection
• Version 1.2: 2019-09-18
  Changes: Data collection
• Version 1.3: 2020-07-29
  Changes: Database references
• Version 1.4: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary