7MRP | pdb_00007mrp

MicroED structure of lysozyme from milled crystals at 1.75A

• PDB DOI: https://doi.org/10.2210/pdb7MRP/pdb
• EM Map EMD-23957: EMDB EMDataResource

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


• Deposited: 2021-05-07 Released: 2022-05-11 
• Deposition Author(s): Martynowycz, M.W., Gonen, T.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 1.75 Å
• R-Value Free: 
  0.213 (Depositor) 
• R-Value Work: 
  0.168 (Depositor) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Preparing crystalline lamellae by focused ion-beam milling for microcrystal electron diffraction (MicroED) experiments

Martynowycz, M.W., Gonen, T.

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: 14.46 kDa 
• Atom Count: 1,084 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	B [auth A], C [auth A], D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 1.75 Å
• R-Value Free:  0.213 (Depositor) 
• R-Value Work:  0.168 (Depositor) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.62	α = 90
b = 77.62	β = 90
c = 37.87	γ = 90

Software Package:

Software Name	Purpose
phenix.refine	refinement
PHENIX	refinement

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-05-11 
Deposition Author(s): Martynowycz, M.W., Gonen, T.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41GM136508

Revision History  

• Version 1.0: 2022-05-11
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Refinement description, Structure summary