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Related Concept Videos

Crystal Field Theory - Octahedral Complexes02:58

Crystal Field Theory - Octahedral Complexes

Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
Crystal Density01:19

Crystal Density

The crystal lattice structure of a material allows us to determine how many molecules exist in its unit cell. With this information, alongside the unit-cell parameters - three distance parameters (a, b, c) and three angular parameters (α, β, γ).Density (ρ) = (Z × M) / (a × b × c × NA)where:Z is the number of formula units per unit cellM is the molar mass of the substancea, b, and c are the edge lengths of the unit cellNA is Avogadro’s numberFor a simple cubic lattice, atoms are located only at...
Crystal Field Theory - Tetrahedral and Square Planar Complexes02:46

Crystal Field Theory - Tetrahedral and Square Planar Complexes

Tetrahedral Complexes
Crystal field theory (CFT) is applicable to molecules in geometries other than octahedral. In octahedral complexes, the lobes of the dx2−y2 and dz2 orbitals point directly at the ligands. For tetrahedral complexes, the d orbitals remain in place, but with only four ligands located between the axes. None of the orbitals points directly at the tetrahedral ligands. However, the dx2−y2 and dz2 orbitals (along the Cartesian axes) overlap with the ligands less than the dxy,...
Ionic Crystal Structures02:42

Ionic Crystal Structures

Ionic crystals consist of two or more different kinds of ions that usually have different sizes. The packing of these ions into a crystal structure is more complex than the packing of metal atoms that are the same size.
Most monatomic ions behave as charged spheres, and their attraction for ions of opposite charge is the same in every direction. Consequently, stable structures for ionic compounds result (1) when ions of one charge are surrounded by as many ions as possible of the opposite...
Crystal Growth: Principles of Crystallization01:25

Crystal Growth: Principles of Crystallization

Crystallization is a phase transformation process in which crystals are precipitated from a supersaturated solution or formed from other sources. During crystallization, atoms or molecules arrange themselves into a well-defined, rigid crystal lattice to minimize energy.
Initiating crystallization involves manipulating the concentration of the solute and the temperature of the solution. Since crystal growth occurs when the ratio of concentration and solubility of the solute in the solvent – the...
Contact-dependent Signaling01:19

Contact-dependent Signaling

Contact-dependent signaling, as the name suggests, requires that communicating cells be in direct contact with each other. This is achieved either through receptor-ligand interactions or by specialized cytoplasmic channels that allow the flow of small molecules between cells. In animal cells, channels called gap junctions facilitate contact-dependent signaling in certain tissues, whereas, plasmodesmata perform a similar function in plants.
Gap Junctions
In animal cells, gap junctions are formed...

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Related Experiment Video

Updated: Jun 23, 2026

Crystallization of Membrane Proteins in Lipidic Mesophases
11:53

Crystallization of Membrane Proteins in Lipidic Mesophases

Published on: March 28, 2011

Crystal contacts as nature's docking solutions.

Evgeny Krissinel1

  • 1European Bioinformatics Institute, Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom. keb@ebi.ac.uk

Journal of Computational Chemistry
|May 8, 2009
PubMed
Summary

Crystal packing may misrepresent natural protein interactions, especially for weakly bound dimers. This study quantifies this misrepresentation risk, crucial for understanding protein structures in solution.

Area of Science:

  • Structural biology
  • Biophysics
  • Computational biology

Background:

  • Crystal contacts are often assumed to reflect natural macromolecular interactions.
  • However, crystal structures may favor non-specific contacts over biologically relevant ones for energetic stability.

Purpose of the Study:

  • To assess the degree to which crystal packing misrepresents natural protein dimers found in solution.
  • To develop a quantitative framework for interpreting docking failures in structural biology.

Main Methods:

  • A large-scale docking experiment was conducted.
  • Analysis of docking failure rates, accounting for calculation errors and crystal misrepresentation effects.
  • Theoretical framework based on thermodynamic equilibrium of dimeric configurations.

More Related Videos

Optimizing the Growth of Endothiapepsin Crystals for Serial Crystallography Experiments
09:52

Optimizing the Growth of Endothiapepsin Crystals for Serial Crystallography Experiments

Published on: February 4, 2021

Harvesting and Cryo-cooling Crystals of Membrane Proteins Grown in Lipidic Mesophases for Structure Determination by Macromolecular Crystallography
18:45

Harvesting and Cryo-cooling Crystals of Membrane Proteins Grown in Lipidic Mesophases for Structure Determination by Macromolecular Crystallography

Published on: September 2, 2012

Related Experiment Videos

Last Updated: Jun 23, 2026

Crystallization of Membrane Proteins in Lipidic Mesophases
11:53

Crystallization of Membrane Proteins in Lipidic Mesophases

Published on: March 28, 2011

Optimizing the Growth of Endothiapepsin Crystals for Serial Crystallography Experiments
09:52

Optimizing the Growth of Endothiapepsin Crystals for Serial Crystallography Experiments

Published on: February 4, 2021

Harvesting and Cryo-cooling Crystals of Membrane Proteins Grown in Lipidic Mesophases for Structure Determination by Macromolecular Crystallography
18:45

Harvesting and Cryo-cooling Crystals of Membrane Proteins Grown in Lipidic Mesophases for Structure Determination by Macromolecular Crystallography

Published on: September 2, 2012

Main Results:

  • Docking failure rates can be quantitatively interpreted by considering errors and misrepresentation.
  • Weakly bound protein complexes (K(D) >= 100 microM), comprising ~20% of Protein Data Bank dimers, have >50% probability of misrepresentation in crystals.
  • A probability estimate for misrepresentation was derived.

Conclusions:

  • Crystal structures may not accurately represent all biologically relevant protein-protein interactions, particularly for weak interactions.
  • The developed theoretical framework can be applied to other experimental studies of systems in thermodynamic equilibrium.
  • Caution is advised when interpreting crystal contacts as definitive representations of in-solution interactions.