Method for modelling the electron density of a crystal

• US 5,200,910 A
• Filed: 01/30/1991
• Issued: 04/06/1993
• Est. Priority Date: 01/30/1991
• Status: Expired due to Term

• Current Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford Management Co.)
• Original Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford Management Co.)
• Inventors: Subbiah, Subramanian
• Primary Examiner(s): Black, Thomas G.
• Assistant Examiner(s): Ramirez, Ellis B.
• Application Number:
  US07/648,788
• Time in Patent Office: 797 Days
• Field of Search: 364/378, 364/499, 364/496, 364/498, 364/554, 364/560
• US Class Current: 703/2
• CPC Class Codes: C07K 1/306 by crystallization
• CPC Class Codes: G16B 15/00 ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment

Abstract

A method for modelling the electron density distribution of a macromolecule in a defined asymmetric unit of a crystal lattice having locations of uniformly diffracting electron density includes the steps of: producing an initial distribution of scattering bodies within a asymmetric unit having the same dimensions as the defined asymmetric unit; calculating scattering amplitudes of the initial distribution and determining the correlation between the calculated scattering amplitudes and the normalized amplitudes; moving at least one of the scattering bodies within the asymmetric unit to create a modified distribution; calculating scattering amplitudes and phases of the modified distribution and determining the correlation between the calculated amplitudes and the normalized values; and producing a final distribution of scattering bodies by repeating moving and calculating steps until the correlation between the calculated scattering amplitudes and the normalized amplitudes is effectively maximized, the final distribution of scattering bodies defining the electron density of the crystal.

Claims

1. A diffractometer system for generating an image of the electron density distribution of a macromolecule crystal, the system comprising:

(a) a source of radiation that diffracts when directed onto the macromolecule crystal;

(b) a detector for collecting an intensity versus position diffraction pattern of the macromolecule crystal;

(c) a processor for converting the diffraction pattern of the crystal into the electron density distribution of the macromolecule crystal, the processor including;

(i) means for determining the asymmetric unit of the crystal;

(ii) means for distributing a number of scattering bodies within the asymmetric unit;

(iii) means for repeatedly generating a scattering amplitude pattern of the scattering bodies, correlating that pattern against the diffraction pattern of the crystal, and moving the scattering bodies a fixed distance to increase the correlation between the patterns of the crystal and the scatterers;

(iv) means for reducing the size of the fixed distance in iii; and

(v) means for ending step iii after the size of the fixed distance reaches a predetermined value, and

(d) a graphical display device for generating an image of the three-dimensional electron density distribution of the crystal, wherein the arrangement of scattering bodies in the ending distribution represents the electron density distribution of the macromolecule crystal.

2. The system recited in claim 1 further comprising a crystal of the macromolecule.

3. The system recited in claim 1 wherein the number of scattering bodies distributed in the asymmetric unit is less than the number of non-hydrogen atoms of the macromolecule crystal in the asymmetric unit.

4. The system recited in claim 1 wherein the scattering bodies are moved in a random direction.

5. The system recited in claim 4 wherein the random directions are parallel to the axes defined by the crystal lattice asymmetric unit.

6. The system recited in claim 1 further comprising means for calculating a correlation coefficient between the scattering body amplitude pattern and the crystal diffraction pattern.

7. The system recited in claim 1 wherein the scattering bodies are spherical and the centers of any two of the spherical scattering bodies are separated by at least a distance equal to the sum of their respective radii.

8. The system recited in claim 1 wherein the scattering bodies in said final distribution occupy locations defining uniformly scattering electron density and the scattering bodies do not occupy space defining electron density of the macromolecule in the crystal lattice.

9. A system for generating an image of the electron density distribution of a macromolecule crystal in a defined asymmetric unit of a crystal lattice, the system comprising

(a) means for converting a diffraction pattern of the macromolecule crystal into computer usable data, the diffraction pattern obtained with a diffractometer;

(b) means for determining the asymmetric unit of the crystal from the computer usable data;

(c) means for distributing a number of scattering bodies within the asymmetric unit;

(d) means for repeatedly generating a scattering amplitude pattern of the scattering bodies, correlating that pattern against the diffraction pattern of the crystal, and moving the scattering bodies a fixed distance to increase the correlation between the patterns of the crystal and the scatterers;

(e) means for reducing the size of the fixed distance in c; and

(f) means for ending step c after the fixed distance reaches a predetermined value; and

(g) means for graphically displaying images of the electron density distribution of the macromolecule crystal.

10. The system recited in claim 9 wherein the number of scattering bodies distributed in the asymmetric unit is less than the number of non-hydrogen atoms of the macromolecule crystal in the asymmetric unit.

11. The system recited in claim 9 wherein said scattering bodies are spherical and the centers of any two of the spherical scattering bodies are separated by at least a distance equal to the sum of their respective radii.

12. A method of generating an image of a macromolecule crystal, the method including the following steps:

(a) converting diffraction data of the macromolecule crystal into computer usable normalized amplitudes, the data being produced with a diffractometer;

(b) determining the dimensions of an asymmetric unit of the crystal;

(c) producing an initial distribution of scattering bodies within an asymmetric unit having the same dimensions as the asymmetric unit determined in step (b);

(d) calculating scattering amplitudes of the initial distribution and determining the correlation between the calculated scattering amplitudes and the computer usable normalized amplitudes from the diffraction data;

(e) moving at least one of said scattering bodies within the asymmetric unit a predefined distance to create a modified distribution;

(f) calculating scattering amplitudes of said modified distribution and determining the correlation between said calculated amplitudes and the normalized amplitudes;

(g) producing a final distribution of scattering bodies by repeating steps (e) and (f), and during at least one step, reducing the predefined distance in step (e), until the correlation between said calculated scattering amplitudes and the normalized amplitudes is effectively maximized, said final distribution of scattering bodies representing the electron density of the crystal; and

(h) graphically displaying an image of the final distribution of scattering bodies.

13. The method recited in claim 12 wherein the step of reducing the predefined distance is repeated until the distance is reduced to a predetermined final distance.

14. The method recited in claim 12 wherein the scattering bodies are translated in a random direction.

15. The method recited in claim 14 wherein the random translation direction is parallel to the axes defined by the asymmetric unit of the crystal.

16. The method recited in claim 12 wherein the steps of determining the correlation between the calculated scattering amplitudes and the normalized amplitudes includes calculating a correlation coefficient between the calculated amplitudes and the normalized amplitudes.

17. The method recited in claim 16 wherein the correlation coefficient is the Pearson coefficient.

18. The method recited in claim 16 wherein the correlation coefficient is an R-value.

19. The method recited in claim 12 wherein the scattering bodies are spherical and the centers of any two spherical scattering bodies are separated by at least a distance equal to the sum of their respective radii.

20. The method recited in claim 12 wherein the scattering bodies in the final distribution occupy locations defining uniformly scattering electron density, and the unoccupied space defines electron density of the macromolecule in the crystal.

21. A method of generating an image of a macromolecule crystal from diffraction data for the macromolecule, the method including the following steps:

(a) receiving the diffraction data from a diffractometer;

(b) determining the dimensions of an asymmetric unit of the crystal from the diffraction data;

(c) converting a portion of the diffraction data for the macromolecule into normalized amplitudes;

(d) randomly distributing a plurality of scattering bodies in a representation of the asymmetric unit of the macromolecule crystal, the number of bodies in the asymmetric unit being less than the number of non-hydrogen atoms in the macromolecule crystal;

(e) moving the plurality of scattering bodies by predetermined distances into a final distribution, whereby the fit between the scattering amplitudes of the final distribution and the amplitudes of the diffraction pattern of the crystal is effectively maximized, the final distribution representing an image of the macromolecule crystal;

(f) displaying a representation of the final distribution of scattering bodies.

22. The method recited in claim 21 further comprising steps of refining the random distribution of scattering bodies into the final distribution, the refining steps including:

(i) reducing the predetermined distances;

(ii) moving at least one of the scattering bodies by the reduced distance within the asymmetrical unit to modify the distribution;

(iii) calculating scattering amplitudes of the modified distribution and determining the correlation between said calculated amplitudes and the normalized amplitudes; and

(iv) producing the final distribution of scattering bodies by repeating steps (b) and (c) until the correlation between the calculated amplitudes of the distribution and the normalized amplitudes is effectively maximized.

23. The method recited in claim 22 wherein the refining steps are repeated until the predetermined distance is reduced to a final distance.

24. The method recited in claim 22 wherein the steps of determining the correlation between the calculated amplitudes of the scattering bodies and the normalized amplitudes includes calculating a correlation coefficient between the calculated amplitudes and the normalized amplitudes.