scholarly journals The early history of cryo-cooling for macromolecular crystallography

IUCrJ ◽  
2020 ◽  
Vol 7 (2) ◽  
pp. 148-157 ◽  
Author(s):  
David J. Haas
Keyword(s):  
Lactate Dehydrogenase ◽  
Radiation Damage ◽  
Analytical Data ◽  
Data Bank ◽  
Protein Crystal ◽  
Protein Crystals ◽  
X Ray ◽  
Royal Institution ◽  
History Of ◽  
Lysozyme Crystals

This paper recounts the first successful cryo-cooling of protein crystals that demonstrated the reduction in X-ray damage to macromolecular crystals. The project was suggested by David C. Phillips in 1965 at the Royal Institution of Great Britain and continued in 1967 at the Weizmann Institute of Science, where the first cryo-cooling experiments were performed on lysozyme crystals, and was completed in 1969 at Purdue University on lactate dehydrogenase crystals. A 1970 publication in Acta Crystallographica described the cryo-procedures, the use of cryo-protectants to prevent ice formation, the importance of fast, isotropic cryo-cooling and the collection of analytical data showing more than a tenfold decrease in radiation damage in cryo-cooled lactate dehydrogenase crystals. This was the first demonstration of any method that reduced radiation damage in protein crystals, which provided crystallographers with suitable means to employ synchrotron X-ray sources for protein-crystal analysis. Today, fifty years later, more than 90% of the crystal structures deposited in the Protein Data Bank have been cryo-cooled.

scholarly journals RABDAM: quantifying specific radiation damage in individual protein crystal structures

2018 ◽  
Vol 51 (2) ◽  
pp. 552-559 ◽  
Author(s):  
Kathryn L. Shelley ◽  
Thomas P. E. Dixon ◽  
Jonathan C. Brooks-Bartlett ◽  
Elspeth F. Garman
Keyword(s):  
Radiation Damage ◽  
Open Source Software ◽  
Structural Changes ◽  
Data Bank ◽  
Protein Crystal ◽  
Standard Format ◽  
X Ray ◽  
Extent Of Damage ◽  
Local Packing Density

Radiation damage remains one of the major limitations to accurate structure determination in protein crystallography (PX). Despite the use of cryo-cooling techniques, it is highly probable that a number of the structures deposited in the Protein Data Bank (PDB) have suffered substantial radiation damage as a result of the high flux densities of third generation synchrotron X-ray sources. Whereas the effects of global damage upon diffraction pattern reflection intensities are readily detectable, traditionally the (earlier onset) site-specific structural changes induced by radiation damage have proven difficult to identify within individual PX structures. More recently, however, development of theBDamagemetric has helped to address this problem.BDamageis a quantitative, per-atom metric identifies potential sites of specific damage by comparing the atomicB-factor values of atoms that occupy a similar local packing density environment in the structure. Building upon this past work, this article presents a program,RABDAM, to calculate theBDamagemetric for all selected atoms within any standard-format PDB or mmCIF file.RABDAMprovides several useful outputs to assess the extent of damage suffered by an input PX structure. This free and open-source software will allow assessment and improvement of the quality of PX structures both previously and newly deposited in the PDB.

scholarly journals Radiation damage in protein crystals examined under various conditions by different methods

2009 ◽  
Vol 16 (2) ◽  
pp. 129-132 ◽  
Author(s):  
Elspeth F. Garman ◽  
Colin Nave
Keyword(s):  
Radiation Damage ◽  
Electronic State ◽  
Room Temperature ◽  
Protein Crystal ◽  
Protein Crystals ◽  
X Rays ◽  
X Ray Diffraction ◽  
Radiation Physics ◽  
X Ray ◽  
The Past

Investigation of radiation damage in protein crystals has progressed in several directions over the past couple of years. There have been improvements in the basic procedures such as calibration of the incident X-ray intensity and calculation of the dose likely to be deposited in a crystal of known size and composition with this intensity. There has been increased emphasis on using additional techniques such as optical, Raman or X-ray spectroscopy to complement X-ray diffraction. Apparent discrepancies between the results of different techniques can be explained by the fact that they are sensitive to different length scales or to changes in the electronic state rather than to movement of atoms. Investigations have been carried out at room temperature as well as cryo-temperatures and, in both cases, with the introduction of potential scavenger molecules. These and other studies are leading to an overall description of the changes which can occur when a protein crystal is irradiated with X-rays at both cryo- and room temperatures. Results from crystallographic and spectroscopic radiation-damage experiments can be reconciled with other studies in the field of radiation physics and chemistry.

Radiation Damage of Protein Crystal in Various X-ray Energies

2007 ◽  
Author(s):  
Nobutaka Shimizu ◽  
Kunio Hirata ◽  
Kazuya Hasegawa ◽  
Go Ueno ◽  
Masaki Yamamoto
Keyword(s):  
Radiation Damage ◽  
Protein Crystal ◽  
X Ray

Pressure-induced high-density amorphous ice in protein crystals

2008 ◽  
Vol 41 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Chae Un Kim ◽  
Yi-Fan Chen ◽  
Mark W. Tate ◽  
Sol M. Gruner
Keyword(s):  
High Pressure ◽  
Ambient Pressure ◽  
Protein Crystallization ◽  
High Density ◽  
Protein Crystal ◽  
Protein Crystals ◽  
X Ray ◽  
Crystallization Solution ◽  
Highly Correlated

Crystal cryocooling has been used in X-ray protein crystallography to mitigate radiation damage during diffraction data collection. However, cryocooling typically increases crystal mosaicity and often requires a time-consuming search for cryoprotectants. A recently developed high-pressure cryocooling method reduces crystal damage relative to traditional cryocooling procedures and eases or eliminates the need to screen for cryoprotectants. It has been proposed that the formation of high-density amorphous (HDA) ice within the protein crystal is responsible for the excellent diffraction quality of the high-pressure cryocooled crystals. This paper reports X-ray data that confirm the presence of HDA ice in the high-pressure cryocooled protein crystallization solution and protein crystals analyzed at ambient pressure. Diffuse scattering with a spacing characteristic of HDA ice is seen at low temperatures. This scattering then becomes characteristic successively to low-density amorphous, cubic and hexagonal ice phases as the temperature is gradually raised from 80 to 230 K, and seems to be highly correlated with the diffraction quality of crystals.

Quantifying X-ray radiation damage in protein crystals at cryogenic temperatures

2006 ◽  
Vol 62 (9) ◽  
pp. 1030-1038 ◽  
Author(s):  
Jan Kmetko ◽  
Naji S. Husseini ◽  
Matthew Naides ◽  
Yevgeniy Kalinin ◽  
Robert E. Thorne
Keyword(s):  
Radiation Damage ◽  
Protein Crystals ◽  
Cryogenic Temperatures ◽  
X Ray

scholarly journals Quantifying X-ray radiation damage in protein crystals

2007 ◽  
Vol 63 (a1) ◽  
pp. s88-s88
Author(s):  
R. E. Thorne ◽  
J. Kmetko ◽  
M. Warkentin ◽  
U. Englich
Keyword(s):  
Radiation Damage ◽  
Protein Crystals ◽  
X Ray

scholarly journals Comparison of the Quality of Protein Crystals Grown by CLPC Seeds Method

Crystals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 501 ◽  
Author(s):  
Li ◽  
Yan ◽  
Liu ◽  
Wu ◽  
Liu ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Protein Crystal ◽  
Protein Crystals ◽  
X Ray Diffraction ◽  
High Quality ◽  
X Ray ◽  
High Quality Protein

We present a systematic quality comparison of protein crystals obtained with and without cross-linked protein crystal (CLPC) seeds. Four proteins were used to conduct the experiments, and the results showed that crystals obtained in the presence of CLPC seeds exhibited a better morphology. In addition, the X-ray diffraction data showed that the CLPC seeds method is a powerful tool to obtain high-quality protein crystals. Therefore, we recommend the use of CLPC seeds in preparing high-quality diffracting protein crystals.

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