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Related Experiment Video

Updated: Nov 9, 2025

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

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

Published on: September 2, 2012

Ice in biomolecular cryocrystallography.

David W Moreau¹, Hakan Atakisi¹, Robert E Thorne¹

¹Physics Department, Cornell University, Ithaca, NY 14853, USA.

Acta Crystallographica. Section D, Structural Biology

|April 7, 2021

Summary

Ice diffraction in cryocooled protein crystals is common. A new method detects ice contamination in protein structure-factor data, revealing that ~16% of PDB entries show ice, influenced by solvent content and cavity size.

Keywords:

ice protein crystallography stacking disorder structure-factor error

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Area of Science:

Structural biology
Crystallography
Materials science

Background:

Diffraction data from cryocooled protein crystals frequently contain ice diffraction patterns.
Ice formation within protein crystals during rapid cooling can complicate structural analysis.

Purpose of the Study:

To develop and validate a revised metric for detecting ice contamination in protein structure-factor data.
To analyze the prevalence and characteristics of ice contamination in a large dataset of protein crystal structures.

Main Methods:

Analysis of ice diffraction patterns from three protein crystals.
Development of a revised ice detection metric based on previous work.
Validation of the metric using diffraction data from the Integrated Resource for Reproducibility in Macromolecular Crystallography.
Application of the metric and improved algorithms to analyze 89,5827 PDB entries.

Main Results:

Ice formed in solvent cavities is a mixture of hexagonal and cubic planes, with cubic fraction increasing with cryoprotectant concentration and cooling rate.
Approximately 16% of cryogenic temperature PDB entries show evidence of ice contamination.
Ice contamination prevalence increases with higher solvent content and larger solvent cavity sizes.
25% of contaminated crystals showed hexagonal ice, suggesting inadequate cooling, while 75% showed stacking-disordered or cubic ice.

Conclusions:

A robust method for detecting ice contamination in protein structure-factor data has been established.
Ice contamination is a significant issue in macromolecular crystallography, affecting a notable percentage of deposited structures.
Understanding ice characteristics (hexagonal vs. cubic) provides insights into cooling protocols and cryoprotectant strategies.