WO2004068415A1 - Procede de reconstruction 3d a resolution elevee - Google Patents

Procede de reconstruction 3d a resolution elevee Download PDF

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Publication number
WO2004068415A1
WO2004068415A1 PCT/SE2004/000075 SE2004000075W WO2004068415A1 WO 2004068415 A1 WO2004068415 A1 WO 2004068415A1 SE 2004000075 W SE2004000075 W SE 2004000075W WO 2004068415 A1 WO2004068415 A1 WO 2004068415A1
Authority
WO
WIPO (PCT)
Prior art keywords
crystal
reconstruction
space group
sample
microcrystals
Prior art date
Application number
PCT/SE2004/000075
Other languages
English (en)
Inventor
Ulf Skoglund
Original Assignee
Sidec Technologies Ab
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority claimed from SE0300223A external-priority patent/SE526941C2/sv
Application filed by Sidec Technologies Ab filed Critical Sidec Technologies Ab
Priority to EP04704378A priority Critical patent/EP1590772A1/fr
Priority to US10/544,186 priority patent/US20060261269A1/en
Priority to JP2006502773A priority patent/JP2006517667A/ja
Publication of WO2004068415A1 publication Critical patent/WO2004068415A1/fr

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C30—CRYSTAL GROWTH
    • C30B—SINGLE-CRYSTAL GROWTH; UNIDIRECTIONAL SOLIDIFICATION OF EUTECTIC MATERIAL OR UNIDIRECTIONAL DEMIXING OF EUTECTOID MATERIAL; REFINING BY ZONE-MELTING OF MATERIAL; PRODUCTION OF A HOMOGENEOUS POLYCRYSTALLINE MATERIAL WITH DEFINED STRUCTURE; SINGLE CRYSTALS OR HOMOGENEOUS POLYCRYSTALLINE MATERIAL WITH DEFINED STRUCTURE; AFTER-TREATMENT OF SINGLE CRYSTALS OR A HOMOGENEOUS POLYCRYSTALLINE MATERIAL WITH DEFINED STRUCTURE; APPARATUS THEREFOR
    • C30B35/00—Apparatus not otherwise provided for, specially adapted for the growth, production or after-treatment of single crystals or of a homogeneous polycrystalline material with defined structure

Definitions

  • the present invention relates to a method for achieving a high-resolution 3D reconstruction of a crystal as defined in the preamble of claim 1.
  • the macromolecules are often grown into crystals first.
  • the crystals must be relatively large, typically in the order of magnitude of lO ⁇ m. Such crystals are referred to as macrocrystals.
  • the state of the art procedure for growing crystals is as follows: A buffer solution of the molecule that is to be crystallized is placed in a petri dish, either as a hanging drop or as a sitting drop, surrounded by a similar solution having a higher concentration of e.g. salt. Because of the different concentrations, the solution in the hanging drop or sitting drop will then evaporate, causing a precipitation in the drop comprising a higher concentration of the molecule.
  • the molecule may or may not have crystallized depending on the conditions. The conditions favouring crystallization are not the same for different types of molecules, which means that each type of molecule must be tried out individually.
  • the crystals formed range from very small to, in the best case, some that are large enough to be used.
  • FB filtered backprojection
  • Comet technology as described in the International Patent Application W097/33255, hereby incorporated by reference, (corresponding European Patent Application EP 885 430 and Swedish Patent Application 9601229-9) is used for image reconstruction.
  • the Comet technology is based on the following steps: An initial estimated distribution of the sample is provided
  • a blurred prior prejudice distribution is provided based on the estimated distribution Observed data of the sample is provided
  • a calculating means calculates, for each iteration, a new estimated distribution of the sample using a comparison between the estimated distribution and the observed data of the sample. A new prior prejudice distribution less blurred than the previous one is also calculated. The iterations are continued until the difference between the new estimated distribution and the next preceding estimated distribution is less than a predetermined condition.
  • the repetitive structure of the crystal and, if possible, the space group of the crystal is determined.
  • the geometry is refined and a second 3D reconstruction, using a procedure as described above, for example the combination of filtered backprojection and COMET, is obtained including information about the space group.
  • Information about the quality of the sample can also be used as feedback for the process of growing crystals.
  • the method according to the invention enables the use of microcrystals for achieving 3D reconstructions with a very high resolution, in the order of magnitude of lOA.
  • a major advantage of the method is that molecules that have been modified can be identified and analyzed. Generally, even if a molecule can be crystallized, a small modification such as the addition of a ligand can make it difficult or impossible to crystallize it into macrocrystals. Studies of how ligands are bound to a certain protein are of great interest to protein chemists and with the inventive method this can be studied down to the level of which amino acid the ligand is bound to. The structures can also be compared to protein structures that have already been determined. With the inventive method, therefore, a more flexible handling of ligands is enabled.
  • the inventive method will also enable 3D reconstructions to be made of entirely new types of molecules, like proteoglycans.
  • the samples are examined to see which ones are likely to have any crystals at all. This can be done by looking at them, first with the bare eye or with a light microscope, then for example through a Transmission Electron Microscope (TEM).
  • TEM Transmission Electron Microscope
  • a sample that comprises crystals is selected (S2) and treated as follows: First it is subjected to a process, for example spinning (S3), to crush the crystals into very small crystals, microcrystals, in the order of magnitude of lOOnm. These microcrystals can be treated in the same way as for proteins in a solution to vitrify them for cryo-TEM (S4), that is Place a thin film of the solution comprising the microcrystals on a grid and plunge-freeze it
  • the crystal fragment is identified and analyzed (S7). If it is of poor quality it is discarded (S9) and the process starts again with another sample.
  • the information that the sample is of poor quality can be used as feedback to exclude the conditions under which the sample was placed, and which were not good for growing crystals.
  • the procedure continues as follows:
  • the information about the sample quality can be used as feedback to adjust the conditions used to grow it so that larger crystals can be grown. More importantly for the inventive process, the repetitive structure of the crystal is determined and its space group, if possible (S10).
  • correlation averaging is performed (SI 2) on the repetitive fragments and the regularity of the lattice of the crystal is estimated. This enables an assessment of the quality and also preliminary information about the 3D structure.
  • the process continues as follows: The geometry of the space group is refined, and its orientation is determined (SI 3). Imaging (SI 4) using the methods as discussed above including space group symmetry. This results in a 3D reconstruction having a very high resolution, probably of the same order of magnitude as what can be achieved for macrocrystals using prior art methods. How to do this for an icosahedral structure has already been described in the International Patent Application W097/33255, hereby incorporated by reference, (corresponding European Patent Application EP 885 430 and Swedish Patent Application 9601229-9).

Landscapes

  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Materials Engineering (AREA)
  • Metallurgy (AREA)
  • Organic Chemistry (AREA)
  • Analysing Materials By The Use Of Radiation (AREA)

Abstract

L'invention concerne un procédé permettant d'effectuer la reconstruction 3D à résolution élevée d'un cristal, qui consiste à faire croître un cristal de manière connue de la technique. Ledit procédé est caractérisé en ce qu'il consiste en des étapes de broyage du cristal en microcristaux, de vitrification d'un échantillon de microcristaux en vue d'une cryoTEM (microscopie électronique à transmission), d'enregistrement d'une série d'inclinaisons et d'obtention d'une première reconstruction 3D au moyen de la procédure FB+COMET. Lorsque l'échantillon est de qualité élevée, la structure répétitive et, si possible, le groupe spatial du cristal sont déterminés. Lorsque le groupe spatial est déterminé, on obtient une seconde reconstruction 3D comprenant des informations relatives audit groupe spatial. Le procédé de l'invention permet d'utiliser des microcristaux pour effectuer de reconstructions 3D à résolution très élevée, de l'ordre de 10Å de magnitude.
PCT/SE2004/000075 2003-01-30 2004-01-22 Procede de reconstruction 3d a resolution elevee WO2004068415A1 (fr)

Priority Applications (3)

Application Number Priority Date Filing Date Title
EP04704378A EP1590772A1 (fr) 2003-01-30 2004-01-22 Procede de reconstruction 3d a resolution elevee
US10/544,186 US20060261269A1 (en) 2003-01-30 2004-01-22 Method for high-resolution 3d reconstruction
JP2006502773A JP2006517667A (ja) 2003-01-30 2004-01-22 高解像度三次元再構成方法

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US31991503P 2003-01-30 2003-01-30
SE0300223A SE526941C2 (sv) 2003-01-30 2003-01-30 Förfarande för 3D-återskapning med hög upplösning
SE0300223-5 2003-01-30
US60/319,915 2003-01-30

Publications (1)

Publication Number Publication Date
WO2004068415A1 true WO2004068415A1 (fr) 2004-08-12

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/SE2004/000075 WO2004068415A1 (fr) 2003-01-30 2004-01-22 Procede de reconstruction 3d a resolution elevee

Country Status (3)

Country Link
EP (1) EP1590772A1 (fr)
JP (1) JP2006517667A (fr)
WO (1) WO2004068415A1 (fr)

Cited By (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2007114772A1 (fr) * 2006-04-04 2007-10-11 Sidec Technologies Ab Tomographie électronique étendue
WO2009070120A1 (fr) * 2007-11-30 2009-06-04 Sidec Technologies Ab Régularisation lp de représentations éparses appliquée à des procédés de détermination de structures en biologie moléculaire/chimie structurale
US9594032B2 (en) 2013-03-13 2017-03-14 Okinawa Institute Of Science And Technology School Corporation Extended field iterative reconstruction technique (EFIRT) for correlated noise removal

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5241471A (en) * 1989-12-20 1993-08-31 General Electric Cgr S.A. Method of multi-scale reconstruction of the image of the structure of a body at an increased speed
US5400255A (en) * 1994-02-14 1995-03-21 General Electric Company Reconstruction of images from cone beam data
US6418243B1 (en) * 1996-03-07 2002-07-09 B. Ulf Skoglund Apparatus and method for providing high fidelity reconstruction of an observed sample
WO2002071336A1 (fr) * 2001-03-05 2002-09-12 Sidec Technologies Ab Procede de localisation et d'identification d'epitopes
US6507633B1 (en) * 2001-02-15 2003-01-14 The Regents Of The University Of Michigan Method for statistically reconstructing a polyenergetic X-ray computed tomography image and image reconstructor apparatus utilizing the method

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5241471A (en) * 1989-12-20 1993-08-31 General Electric Cgr S.A. Method of multi-scale reconstruction of the image of the structure of a body at an increased speed
US5400255A (en) * 1994-02-14 1995-03-21 General Electric Company Reconstruction of images from cone beam data
US6418243B1 (en) * 1996-03-07 2002-07-09 B. Ulf Skoglund Apparatus and method for providing high fidelity reconstruction of an observed sample
US6507633B1 (en) * 2001-02-15 2003-01-14 The Regents Of The University Of Michigan Method for statistically reconstructing a polyenergetic X-ray computed tomography image and image reconstructor apparatus utilizing the method
WO2002071336A1 (fr) * 2001-03-05 2002-09-12 Sidec Technologies Ab Procede de localisation et d'identification d'epitopes

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
COP M. ET AL: "A Multi-resolution approach to the 3D reconstruction of 50S ribosomefrom an EM-Tilt series solving the alignment problem without gold particles", DEPARTMENT OF MEDICAL AND BIOLOGICAL INFORMATICS, 1990, HEIDELBERG, pages 733 - 737, XP010020340 *

Cited By (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2007114772A1 (fr) * 2006-04-04 2007-10-11 Sidec Technologies Ab Tomographie électronique étendue
US7880142B2 (en) 2006-04-04 2011-02-01 Sidec Technologies Ab Extended electron tomography
WO2009070120A1 (fr) * 2007-11-30 2009-06-04 Sidec Technologies Ab Régularisation lp de représentations éparses appliquée à des procédés de détermination de structures en biologie moléculaire/chimie structurale
US9594032B2 (en) 2013-03-13 2017-03-14 Okinawa Institute Of Science And Technology School Corporation Extended field iterative reconstruction technique (EFIRT) for correlated noise removal
US9733199B2 (en) 2013-03-13 2017-08-15 Okinawa Institute Of Science And Technology School Corporation Extended field iterative reconstruction technique (EFIRT) for correlated noise removal

Also Published As

Publication number Publication date
JP2006517667A (ja) 2006-07-27
EP1590772A1 (fr) 2005-11-02

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