8QF3 | pdb_00008qf3

1.25-A structure of anti-Arc nanobody H11

• PDB DOI: https://doi.org/10.2210/pdb8QF3/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Vicugna pacos
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-09-02 Released: 2024-03-13 
• Deposition Author(s): Godoy Munoz, J.M., Kursula, P.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.232 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

1.25-A structure of anti-Arc nanobody H11

Godoy Munoz, J.M., Kursula, P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 28.16 kDa 
• Atom Count: 2,133 
• Modeled Residue Count: 252 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody H11	A [auth E], B [auth A]	128	Vicugna pacos	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.232 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.17	α = 90
b = 57.17	β = 90
c = 145.64	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-03-13 
Deposition Author(s): Godoy Munoz, J.M., Kursula, P.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-03-13
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary