Radiation Damage of Protein Crystal in Various X-ray Energies

Recently, there has been a growing interest in adapting serial microcrystallography (SMX) experiments to existing storage ring (SR) sources. For very small crystals, however, radiation damage occurs before sufficient numbers of photons are diffracted to determine the orientation of the crystal. The challenge is to merge data from a large number of such `sparse' frames in order to measure the full reciprocal space intensity. To simulate sparse frames, a dataset was collected from a large lysozyme crystal illuminated by a dim X-ray source. The crystal was continuously rotated about two orthogonal axes to sample a subset of the rotation space. With the EMC algorithm [expand–maximize–compress; Loh & Elser (2009).Phys. Rev. E,80, 026705], it is shown that the diffracted intensity of the crystal can still be reconstructed even without knowledge of the orientation of the crystal in any sparse frame. Moreover, parallel computation implementations were designed to considerably improve the time and memory scaling of the algorithm. The results show that EMC-based SMX experiments should be feasible at SR sources.

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RABDAM: quantifying specific radiation damage in individual protein crystal structures

Journal of Applied Crystallography ◽

10.1107/s1600576718002509 ◽

2018 ◽

Vol 51 (2) ◽

pp. 552-559 ◽

Cited By ~ 4

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.

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Intact structure determination of a highly radiation sensitive protein at SACLA

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314094303 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C569-C569

Author(s):

Hideo Ago ◽

Kunio Hirata ◽

Kyoko Shinzawa-Itoh ◽

Naomine Yano ◽

Tomitake Tsukihara ◽

...

Keyword(s):

Crystal Structure ◽

High Resolution ◽

Radiation Damage ◽

Structure Determination ◽

Structural Modification ◽

Crystal Structure Determination ◽

Protein Crystal ◽

X Ray ◽

O2 Reduction

X-ray irradiation on a protein crystal can cause some subtle structural modification on the protein structure even if the radiation dose is much smaller than a dose used for a common crystal structure determination. In some case such structural modification increases ambiguity of structural inspection, and eventually could be an obstacle on the elucidation of structure basis of protein function. Bovine heart cytochrome c oxidase (CcO) is one of such proteins having some problem caused by the radiation damage. The proton pumping of CcO is coupled with O2 reduction at the O2 reduction site, thus accurate structure determination of bound ligand as well as CcO itself is very important. Whereas accurate structure determination was impeded by the immediate photolysis of the peroxide ligand upon X-ray irradiation even at a cryogenic temperature[1]. We developed a goniometer based data collection system for the femtosecond crystallography at SACLA (SPring-8 Angstrom Compact free-electron LAser). The femtosecond crystallography is expected to have an advantage in high-resolution and radiation damage free structure determination of very large protein by combined usage of large crystal and femtosecond intense X-ray pulse. In this presentation we are going to show the result of the femtosecond crystallography on the crystal of CcO having large unit cell dimensions. The close inspection of the electron density map calculated at 1.9 Å resolution showed the femtosecond crystallography worked fine for the high resolution and radiation damage free crystal structure determination of CcO.

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The early history of cryo-cooling for macromolecular crystallography

IUCrJ ◽

10.1107/s2052252519016993 ◽

2020 ◽

Vol 7 (2) ◽

pp. 148-157 ◽

Cited By ~ 2

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.

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

Journal of Synchrotron Radiation ◽

10.1107/s0909049509005238 ◽

2009 ◽

Vol 16 (2) ◽

pp. 129-132 ◽

Cited By ~ 27

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.

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Studies of metaphase chromosomes in the scanning transmission x-ray microscope: Image fidelity, radiation damage and specimen preparation

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100129826 ◽

1992 ◽

Vol 50 (2) ◽

pp. 1038-1039

Author(s):

Shawn Williams ◽

Xiaodong Zhang ◽

Susan Lamm ◽

Jack Van’t Hof

Keyword(s):

Visible Light ◽

Radiation Damage ◽

Cross Section ◽

Imaging Techniques ◽

Dose Range ◽

Specimen Preparation ◽

X Rays ◽

Metaphase Chromosomes ◽

X Ray ◽

Scanning Transmission

The Scanning Transmission X-ray Microscope (STXM) is well suited for investigating metaphase chromosome structure. The absorption cross-section of soft x-rays having energies between the carbon and oxygen K edges (284 - 531 eV) is 6 - 9.5 times greater for organic specimens than for water, which permits one to examine unstained, wet biological specimens with resolution superior to that attainable using visible light. The attenuation length of the x-rays is suitable for imaging micron thick specimens without sectioning. This large difference in cross-section yields good specimen contrast, so that fewer soft x-rays than electrons are required to image wet biological specimens at a given resolution. But most imaging techniques delivering better resolution than visible light produce radiation damage. Soft x-rays are known to be very effective in damaging biological specimens. The STXM is constructed to minimize specimen dose, but it is important to measure the actual damage induced as a function of dose in order to determine the dose range within which radiation damage does not compromise image quality.

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Characterization of defects in tabular silver halide grains

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100178367 ◽

1990 ◽

Vol 48 (4) ◽

pp. 1046-1047

Author(s):

C. Goessens ◽

D. Schryvers ◽

J. Van Landuyt ◽

A. Verbeeck ◽

R. De Keyzer

Keyword(s):

Radiation Damage ◽

Silver Halide ◽

Chemical Characteristics ◽

X Ray ◽

Free Region ◽

Central Defect ◽

Crystallographic Defects ◽

Physical And Chemical ◽

Two Sides

Silver halide grains (AgX, X=Cl,Br,I) are commonly recognized as important entities in photographic applications. Depending on the preparation specifications one can grow cubic, octahedral, tabular a.o. morphologies, each with its own physical and chemical characteristics. In the present study crystallographic defects introduced by the mixing of 5-20% iodide in a growing AgBr tabular grain are investigated. X-ray diffractometry reveals the existence of a homogeneous Ag(Br1-xIx) region, expected to be formed around the AgBr kernel. In fig. 1 a two-beam BF image, taken at T≈100 K to diminish radiation damage, of a triangular tabular grain is presented, clearly showing defect contrast fringes along four of the six directions; the remaining two sides show similar contrast under relevant diffraction conditions. The width of the central defect free region corresponds with the pure AgBr kernel grown before the mixing with I. The thickness of a given grain lies between 0.15 and 0.3 μm: as indicated in fig. 2 triangular (resp. hexagonal) grains exhibit an uneven (resp. even) number of twin interfaces (i.e., between + and - twin variants) parallel with the (111) surfaces. The thickness of the grains and the existence of the twin variants was confirmed from CTEM images of perpendicular cuts.

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Factors in Photographic Emulsions for Low Dose Electron Crystallography

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s143192760000101x ◽

1980 ◽

Vol 38 ◽

pp. 230-231

Author(s):

T.W. Jeng ◽

W. Chiu

Keyword(s):

Radiation Damage ◽

Low Dose ◽

Damage Effect ◽

Photographic Emulsion ◽

Electron Crystallography ◽

Electron Microscopic ◽

X Ray ◽

Signal Contrast ◽

Diffraction Patterns ◽

Photographic Emulsions

With the advances in preparing biological materials in a thin and highly ordered form, and in maintaining them hydrated under vacuum, electron crystallography has become an important tool for biological structure investigation at high resolution (1,2). However, the electron radiation damage would limit the capability of recording reflections with low intensities in an electron diffraction pattern. It has been demonstrated that the use of a low temperature stage can reduce the radiation damage effect and that one can expose the specimen with a higher dose in order to increase the signal contrast (3). A further improvement can be made by selecting a proper photographic emulsion. The primary factors in evaluating the suitability of photographic emulsion for recording low dose diffraction patterns are speed, fog level, electron response at low electron exposure, linearity, and usable range of exposure. We have compared these factors with three photographic emulsions including Kodak electron microscopic plate (EMP), Industrex AA x-ray film (AA x-ray) and Kodak nuclear track film (NTB3).

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