9B7C | pdb_00009b7c

high-resolution ambient temperature structure of lysozyme soaked with sodium iodide

• PDB DOI: https://doi.org/10.2210/pdb9B7C/pdb

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


• Deposited: 2024-03-27 Released: 2024-07-31 
• Deposition Author(s): Wang, H.K., Greisman, J.B., Hekstra, D.R.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.123 (Depositor), 0.120 (DCC) 
• R-Value Work: 
  0.111 (Depositor), 0.110 (DCC) 
• R-Value Observed: 
  0.111 (Depositor) 

Literature

Bayesian Priors for Comparative Crystallography

Hekstra, D.R., Wang, H.K.

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: 14.92 kDa 
• Atom Count: 1,284 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.123 (Depositor), 0.120 (DCC) 
• R-Value Work:  0.111 (Depositor), 0.110 (DCC) 
• R-Value Observed: 0.111 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.405	α = 90
b = 79.405	β = 90
c = 37.837	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
DIALS	data reduction
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-31 
Deposition Author(s): Wang, H.K., Greisman, J.B., Hekstra, D.R.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	DGE 2140743
National Science Foundation (NSF, United States)	United States	DGE1745303
National Institutes of Health/Office of the Director	United States	DP2-GM141000

Revision History  

• Version 1.0: 2024-07-31
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Structure summary