5W6W | pdb_00005w6w

Designing Higher Resolution Self-Assembled 3D DNA Crystals via Strand Terminus Modifications

• PDB DOI: https://doi.org/10.2210/pdb5W6W/pdb
• NAKB: 5W6W

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2017-06-17 Released: 2018-06-27 
• Deposition Author(s): Hernandez, C., Birktoft, J.J., Seeman, N.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.06 Å
• R-Value Free: 
  0.241 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Designing Higher Resolution Self-Assembled 3D DNA Crystals via Strand Terminus Modifications

Hernandez, C., Birktoft, J.J., Seeman, N.C., Ohayon, Y.P., Chandrasekaran, A.R., Abdalla, H.O., Mohsen, M., Sha, R., Chenge, M., Lukeman, P.S., Chaikin, P., Ginell, S.L., Jong, M.A.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 12.8 kDa 
• Atom Count: 859 
• Modeled Residue Count: 42 
• Deposited Residue Count: 42 
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')	A	21	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')	B	7	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')	C	7	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')	D	7	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.06 Å
• R-Value Free:  0.241 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.712	α = 90
b = 106.712	β = 90
c = 94.081	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-06-27 
Deposition Author(s): Hernandez, C., Birktoft, J.J., Seeman, N.C.

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

Revision History  

• Version 1.0: 2018-06-27
  Type: Initial release
  
• Version 1.1: 2019-08-28
  Changes: Data collection, Database references
• Version 1.2: 2022-03-23
  Changes: Author supporting evidence, Database references
• Version 1.3: 2023-10-04
  Changes: Data collection, Refinement description