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Related Concept Videos

X-ray Diffraction of Biological Samples01:10

X-ray Diffraction of Biological Samples

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X-ray diffraction or XRD is an analytical tool that utilizes X-rays to study ordered structures such as crystalline organic and inorganic samples, polycrystalline materials, proteins, carbohydrates, and drugs.
According to Bragg's law, when X-rays strike the sample positioned on a stage, the rays are  scattered by the electron clouds around the sample atoms. The  X-ray diffraction or scattering is caused by constructive interference of the X-ray waves that reflect off the internal...
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X-ray Crystallography02:18

X-ray Crystallography

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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...
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Data Collection by Experiments01:13

Data Collection by Experiments

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Data collection is a systematic method of obtaining, observing, measuring, and analyzing accurate information. An experimental study is a standard method of data collection that involves the manipulation of the samples by applying some form of treatment prior to data collection. It refers to manipulating one variable to determine its changes on another variable. The sample subjected to treatment is known as “experimental units.”
An example of the experimental method is a public...
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Interference and Diffraction02:18

Interference and Diffraction

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Interference is a characteristic phenomenon exhibited by waves. When two electromagnetic waves interact with their peaks and troughs coinciding, a resulting wave with enhanced amplitude is produced. This is known as constructive interference. In this case, the two waves interacting are in phase with each other.
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Model Approaches for Pharmacokinetic Data: Physiological Models01:15

Model Approaches for Pharmacokinetic Data: Physiological Models

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Physiological models in pharmacokinetics are instrumental in understanding the distribution and elimination of drugs within the body. These models describe the drug concentration within target organs, influenced by factors such as drug uptake, tissue volume, and blood flow. Drug uptake is governed by the partition coefficient, which signifies the drug concentration ratio in tissue to that in the blood. The blood flow rate to a specific tissue is expressed as Qt, and the rate of change in tissue...
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Model Approaches for Pharmacokinetic Data: Compartment Models01:14

Model Approaches for Pharmacokinetic Data: Compartment Models

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Compartmental analysis is a widely adopted approach to characterizing drug pharmacokinetics. It uses compartment models that conceptualize the body as a collection of reversibly communicating compartments, each representing a group of tissues exhibiting similar drug distribution characteristics. The movement rate of the drug between these compartments is typically described by first-order kinetics.
Two primary types of compartment models are recognized: mammillary and catenary. The more...
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Related Experiment Video

Updated: Feb 2, 2026

Crystallization of Proteins on Chip by Microdialysis for In Situ X-ray Diffraction Studies
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Refining the macromolecular model - achieving the best agreement with the data from X-ray diffraction experiment.

Ivan G Shabalin1,2, Przemyslaw J Porebski1,2, Wladek Minor1,2

  • 1Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States.

Crystallography Reviews
|November 13, 2018
PubMed
Summary

This tutorial guides novice crystallographers through macromolecular structure refinement, explaining key concepts like R-free and restraints. It offers practical tips for optimizing model refinement and manual corrections using software.

Keywords:
X-ray crystallographyligandsprotein crystal structurerefinementreproducibilitystructural biology

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Area of Science:

  • Structural Biology
  • Crystallography
  • Biochemistry

Background:

  • Macromolecular X-ray crystal structure refinement is complex due to extensive software settings.
  • Inexperienced crystallographers face challenges in achieving optimal refinement results.
  • A need exists for clear guidelines and practical advice in structure refinement.

Purpose of the Study:

  • To provide a tutorial review for refining macromolecular X-ray crystal structures.
  • To offer guidelines for selecting optimal reciprocal-space refinement settings.
  • To present practical tips for manual model correction and interpretation of structural data.

Main Methods:

  • Explanation of core concepts in protein structure refinement.
  • Discussion of R-free, geometrical restraints, and atomic displacement parameter (ADP) restraints.
  • Guidance on refinement weights, ADP parametrizations (anisotropic, TLS), and omit maps.

Main Results:

  • Provides a structured approach to understanding and applying refinement settings.
  • Details practical strategies for manual model correction in Coot.
  • Covers modeling of side-chains, ligand identification, fitting, and refinement in low-density regions.

Conclusions:

  • Empowers less experienced crystallographers to improve structure refinement outcomes.
  • Facilitates better interpretation of electron density maps and model building.
  • Enhances the accuracy and reliability of refined macromolecular structures.