101D

REFINEMENT OF NETROPSIN BOUND TO DNA: BIAS AND FEEDBACK IN ELECTRON DENSITY MAP INTERPRETATION

Structural Biology Knowledgebase: 101D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Observed: 0.163

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 101D

Classification: DNA

Total Structure Weight: 7939.41

Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(CBR)P*GP*CP*G)-3') A, B 12 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NT
Query on NT

B NETROPSIN
C18 H26 N10 O3
IDBIFFKSXLYUOT-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CBR
Query on CBR
A, B DNA LINKING C9 H13 Br N3 O7 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Observed: 0.163
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 24.27 α = 90.00
b = 39.62 β = 90.00
c = 63.57 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 1994-12-14
  • Released Date: 1995-02-27
  • Deposition author(s): Goodsell, D.S., Kopka, M.L., Dickerson, R.E.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4