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Determination of Crystal Structures

Determination of Crystal Structures

In the late 1800s, the revelation that light extended beyond visible wavelengths led to the discovery of X-rays by Wilhelm Roentgen. Recognized as high-energy electromagnetic radiation with short wavelengths, X-rays prompted exploration into their interaction with crystals. Max von Laue proposed in 1912 that the periodic arrangement of atoms, ions, or molecules in crystals would cause them to diffract X-rays, a hypothesis confirmed through experiments with copper sulfate and zinc sulfide...

X-ray Crystallography

X-ray Crystallography

The size of the unit cell and the arrangement of atoms in a crystal may be determined from measurements of the diffraction of X-rays by the crystal, termed X-ray crystallography.
Diffraction
Diffraction is the change in the direction of travel experienced by an electromagnetic wave when it encounters a physical barrier whose dimensions are comparable to those of the wavelength of the light. X-rays are electromagnetic radiation with wavelengths about as long as the distance between neighboring...

Lattice Centering and Coordination Number

Lattice Centering and Coordination Number

The structure of a crystalline solid, whether a metal or not, is best described by considering its simplest repeating unit, which is referred to as its unit cell. The unit cell consists of lattice points that represent the locations of atoms or ions. The entire structure then consists of this unit cell repeating in three dimensions. The three different types of unit cells present in the cubic lattice are illustrated in Figure 1.
Types of Unit Cells
Imagine taking a large number of identical...

Structures of Solids

Structures of Solids

Solids in which the atoms, ions, or molecules are arranged in a definite repeating pattern are known as crystalline solids. Metals and ionic compounds typically form ordered, crystalline solids. A crystalline solid has a precise melting temperature because each atom or molecule of the same type is held in place with the same forces or energy. Amorphous solids or non-crystalline solids (or, sometimes, glasses) which lack an ordered internal structure and are randomly arranged. Substances that...

Unit Cells

Unit Cells

A crystal's internal structure is an orderly array of atoms, ions, or molecules, and the details of this array significantly influence the solid's properties. In a crystal, periodically repeating 'structural motifs' - which could be atoms, molecules, or groups thereof - create a 'space lattice.' This is essentially a three-dimensional, infinite array of points, each surrounded by its neighbors in an identical way, forming the basic structure of the crystal.A 'unit cell' is a theoretical...

Lattice Energies of Ionic Crystals

Lattice Energies of Ionic Crystals

Lattice energy represents the energy released when gaseous cations and anions combine to form an ionic solid, reflecting the strength of electrostatic interactions within the crystal. This process is fundamentally governed by Coulombic attraction between oppositely charged ions, where the potential energy varies inversely with the interionic distance and directly with the product of ionic charges. As ions approach one another, the electrostatic energy becomes increasingly negative, indicating a...

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Updated: Jul 11, 2026

Assessing Two-dimensional Crystallization Trials of Small Membrane Proteins for Structural Biology Studies by Electron Crystallography

Assessing Two-dimensional Crystallization Trials of Small Membrane Proteins for Structural Biology Studies by Electron Crystallography

Published on: October 29, 2010

Automatic lattice determination for two-dimensional crystal images.

Xiangyan Zeng¹, Bryant Gipson, Zi Yan Zheng

¹Molecular & Cellular Biology, Briggs Hall, College of Biological Sciences, University of California at Davis, 1 Shields Ave., Davis, CA 95616, USA.

Journal of Structural Biology

|October 2, 2007

Summary

This summary is machine-generated.

This study introduces three automated programs for electron crystallography, simplifying the determination of reciprocal lattice parameters from 2D crystal images. This advancement aids in analyzing membrane protein structures.

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Area of Science:

Structural Biology
Biophysics
Crystallography

Background:

Electron crystallography is crucial for determining the structure of periodic samples, including membrane proteins.
Accurate analysis of electron crystallography data requires precise determination of reciprocal lattice parameters from Fourier transforms of images.
Manual determination of these parameters can be complex and time-consuming.

Purpose of the Study:

To develop an automated method for determining reciprocal lattice parameters from 2D crystal images.
To provide a user-friendly software package for accelerating the analysis of electron crystallography data.
To improve the efficiency and accuracy of structural determination for periodic samples.

Main Methods:

Development of a software package named 2dx, comprising three programs: 2dx_peaksearch, 2dx_findlat, and 2dx_getlat.
2dx_peaksearch identifies Fourier peak coordinates from processed diffraction patterns.
2dx_findlat and 2dx_getlat utilize these coordinates, along with optional real-space unit cell dimensions and sample tilt information, to determine lattice parameters.

Main Results:

The developed programs successfully automate the determination of reciprocal lattice parameters from 2D crystal images.
The software package provides options for lattice determination with or without prior knowledge of unit cell dimensions.
The 2dx software package is publicly available at http://2dx.org.

Conclusions:

The 2dx software package offers an efficient and automated solution for reciprocal lattice determination in electron crystallography.
This tool significantly aids researchers in the structural analysis of membrane proteins and other periodic samples.
The automation streamlines the image processing workflow, making complex structural biology studies more accessible.