Device, system, method, and program for calculating turning radius

Abstract

To provide a gyration radius calculation device, system, method and program for calculating a radius of gyration for a polymer in a solution that has a dynamically varying structure as a final calculated value.SOLUTION: A gyration radius calculation device for calculating a radius of gyration for a polymer molecule in solution includes an electron density map generation unit that generates multiple electron density maps from the actual X-ray scattering profile obtained by measuring the sample, and a theoretical size calculation unit that creates a plot of a dynamic radius of rotation of the molecule calculated based on the multiple electron density maps for each of multiple voxel sizes as a second plot, and calculates an extrapolated value at which the voxel size becomes zero on a regression line of the second plot as a final calculated value of the dynamic radius of rotation of the molecule.SELECTED DRAWING: Figure 9

Description

[Technical Field]

[0001] The present invention relates to a three-dimensional electron density map identification apparatus, system, method, and program for identifying a three-dimensional electron density map of polymers in a solution. [Background technology]

[0002] Extensive research has been conducted on methods for observing biomolecules in solution. When X-rays are shone on biomolecules that are freely moving in solution, a ring-shaped scattered light is produced rather than a spot. A technique is known that detects this scattered light and obtains a three-dimensional electron density map of the target molecule from the resulting measured X-ray scattering profile (Non-Patent Literature 1).

[0003] The method described in Non-Patent Document 1 represents the volume of a cube in real space containing particles as voxels of a discretized cube in an N×N×N grid, and calculates an electron density map by iteratively searching for structure factors based on X-ray scattering data obtained from the sample. [Prior art documents] [Non-patent literature]

[0004] [Non-Patent Document 1] Thomas D Grant, "Ab initio electron density determination directly from solution scattering data", Nature Methods volume 15, 29 January 2018, pages191-193 [Overview of the project] [Problems that the invention aims to solve]

[0005] However, the method described in Non-Patent Document 1 only yields an electron density map that averages multiple structures. Therefore, while a reasonable electron density map can be calculated when analyzing the morphology of rigid molecules, in the case of flexible molecules, the dynamic morphology of the molecule is averaged, and the electron density that should be obtained is not calculated.

[0006] This invention has been made in view of these circumstances, and aims to provide an electron density map identification device, system, method, and program that can reproduce the electron density map of a polymer in a solution that has a structure with dynamic fluctuations. [Means for solving the problem]

[0007] (1) To achieve the above objective, the present invention provides an electron density map identification device for identifying the electron density map of a polymer in a solution, comprising: an electron density map generation unit that generates a plurality of electron density maps from an actual measured X-ray scattering profile obtained by measuring a sample; an index calculation unit that calculates an index representing the degree of agreement between the calculated X-ray scattering profile calculated from each of the plurality of electron density maps and the actual measured X-ray scattering profile; and an electron density map selection unit that selects a representative electron density map from the plurality of electron density maps based on the calculated index.

[0008] (2) The electron density map identification device described in (1) above further comprises a correlation determination unit that creates a first plot of parameters representing molecular size with respect to the calculated index for each of the plurality of electron density maps and determines whether or not there is a correlation between the first plots, and the electron density map selection unit is characterized in that it does not select the representative electron density map if there is no correlation between the first plots.

[0009] (3) Furthermore, the electron density map identification device described in (2) above is further equipped with a trend analysis unit that performs multivariate analysis on the distribution of the first plots when there is no correlation between the first plots, and the electron density map generation unit is characterized in that it generates the multiple electron density maps by changing the conditions when there is a trend in the distribution of the first plots.

[0010] (4) Furthermore, in the electron density map identification device described in (2) above, the correlation determination unit creates the first plot when there is no correlation between the first plots, and the electron density map generation unit generates the multiple electron density maps under conditions based on user instructions.

[0011] (5) Furthermore, in the electron density map identification device described in any of (1) to (4) above, the electron density map generation unit is characterized in that it generates each of the plurality of electron density maps one by one in an iterative process according to the settings.

[0012] (6) Furthermore, in the electron density map identification device described in any of (1) to (4) above, the electron density map generation unit is characterized in that it generates each of the plurality of electron density maps simultaneously in parallel processing according to the settings.

[0013] (7) Furthermore, the electron density map identification device described in any of (1) to (6) above further comprises: a theoretical size calculation unit that creates a second plot of parameters representing the calculated molecular size with respect to the voxel size for each of the plurality of electron density maps and calculates a calculated value of the parameter representing the molecular size of the polymer in the solution using the second plot; and a measured size calculation unit that calculates the parameter representing the molecular size of the polymer in the solution as a measured value from the measured X-ray scattering profile, wherein the electron density map selection unit does not select the representative electron density map if the difference between the calculated value and the measured value is not within a predetermined range.

[0014] (8) Further, the system of the present invention includes an X-ray solution scattering device and the electron density map specifying device according to any one of (1) to (7) above, and the electron density map specifying device specifies an electron density map of a polymer in the solution based on the X-ray scattering profile of the polymer in the solution measured by the X-ray solution scattering device.

[0015] (9) Further, the method of the present invention is a method for specifying an electron density map of a polymer in a solution, and includes steps of generating a plurality of electron density maps from the actually measured X-ray scattering profile obtained by measuring a sample, calculating an index representing the degree of coincidence between the calculated X-ray scattering profile calculated from each of the plurality of electron density maps and the actually measured X-ray scattering profile, and selecting a representative electron density map from the plurality of electron density maps based on the calculated index.

[0016] (10) Further, the program of the present invention is a program for specifying an electron density map of a polymer in a solution, and causes a computer to execute processes of generating a plurality of electron density maps from the actually measured X-ray scattering profile obtained by measuring a sample, calculating an index representing the degree of coincidence between the calculated X-ray scattering profile calculated from each of the plurality of electron density maps and the actually measured X-ray scattering profile, and selecting a representative electron density map from the plurality of electron density maps based on the calculated index.

Brief Description of the Drawings

[0017] [Figure 1] It is a schematic diagram showing the system of the present invention. [Figure 2] It is a perspective view showing an X-ray solution scattering device. [Figure 3] It is a block diagram showing the system of the present invention. [Figure 4] It is a flowchart showing the operation of the electron density map specifying device of the present invention. [Figure 5] It is a graph showing an example of an X-ray scattering profile. [Figure 6] This is a schematic diagram showing an electron density map. [Figure 7] (a) and (b) are graphs showing the ideal distribution and the unanalyzable χ²-Rg(ind) distribution, respectively. [Figure 8] This graph shows the distribution of Rg(ind) relative to χ2 in the example. [Figure 9] This graph shows the extrapolation of Rg(sect) to the voxel size in the example. [Figure 10] This is a list showing the electron density map and processing results in the examples. [Figure 11] (a) to (c) are front, top, and right side views showing the selected electron density maps, respectively. A structural ribbon model obtained separately by X-ray crystallography is superimposed to aid in understanding the obtained electron density maps. [Modes for carrying out the invention]

[0018] Next, embodiments of the present invention will be described with reference to the drawings. To facilitate understanding of the description, the same reference numerals are used for identical components in each drawing, and redundant descriptions are omitted.

[0019] [Electron Density Map Identification System] Figure 1 is a schematic diagram showing the electron density map identification system 10. The electron density map identification system 10 comprises an X-ray solution scattering device 100 and an electron density map identification device 200. The X-ray solution scattering device 100 measures the X-ray solution scattering profile by irradiating a sample S0 with X-rays and detecting the scattered X-rays. The sample S0 is suitable for polymers in solution, especially biopolymers. The sample S0 may also be pharmaceutical molecules, molecular complexes, or structures in solution. Furthermore, by using the X-ray solution scattering method, it is possible to visualize the electron density corresponding to the structural ensemble of biopolymers that cannot be observed in frozen or crystalline states.

[0020] The electron density map identification device 200 consists of a computer 210, an input device 280, and an output device 290, and controls the operation of the X-ray solution scattering device 100, as well as acquiring and processing measurement data from the X-ray solution scattering device 100.

[0021] The X-ray solution scattering apparatus 100 comprises an X-ray generation unit 110, a sample loading mechanism 120, a detector 130, and a control unit 140. The X-ray generation unit 110 has an X-ray source 111 and irradiates the sample S0 with X-rays. The sample loading mechanism 120 sends the sample, which is a polymer or a solution excluding only the polymer, to the X-ray irradiation position. The detector 130 detects the X-rays scattered by the sample S0 and transmits the obtained measurement data to the computer 210.

[0022] Computer 210 is, for example, a PC and consists of a processor that performs processing and memory or a hard disk that stores programs and data. Computer 210 receives user input from input devices 280 such as a keyboard and mouse. On the other hand, computer 210 displays plots, visualized electron density maps, input screens, etc., on output devices 290 such as a display. Computer 210 may also be a server device located in the cloud. Furthermore, from the viewpoint of processing load, the function of controlling the operation of the X-ray solution scattering apparatus 100 and the function of processing measurement data may be separated, with control performed on a PC installed on-site and data processing performed on a server device.

[0023] [X-ray solution scattering device] Figure 2 is a perspective view showing the X-ray solution scattering apparatus 100. The X-ray solution scattering apparatus 100 comprises an X-ray source 111, an optical system 115, a Kratsky block 117, a sample holder tube 125, and a detector 130. The X-ray source 111 is a linear or point source that emits a divergent beam. The optical system 115 is, for example, a KB parallel or series optical system. A pair of Kratsky blocks 117 interact with the X-rays through their respective edges to define one side and the other side of the X-ray beam. This removes parasitic scattering from the irradiated X-rays. The sample holder tube 125 feeds and holds a solution sample from 1 μl to 20 μl. The detector 130 detects the X-rays scattered by the solution sample.

[0024] [Electron density map identification device] Figure 3 is a block diagram showing the electron density map identification system 10. The electron density map identification device 200 acquires data from the X-ray scattering profile measured by the X-ray solution scattering device 100 and identifies the electron density map of the polymer based on the data. The functions of the electron density map identification device 200 are mainly realized by the computer 210.

[0025] The computer 210 includes an input / output control unit 211, a measurement control unit 215, a measurement data storage unit 217, an electron density map generation unit 221, a theoretical scattering intensity calculation unit 225, an index calculation unit 226, a correlation determination unit 231, a trend analysis unit 232, a theoretical size calculation unit 245, a measured size calculation unit 246, an overall determination unit 257, and an electron density map selection unit 258. Each unit can send and receive information via the control bus L.

[0026] The input / output control unit 211 receives input from the input device 280 and controls the output to the output device 290. The input / output control unit 211 can, for example, receive input for measurement conditions or input for conditions to generate multiple electron density maps. The input / output control unit 211 can also output various plots or output an electron density map of a specified polymer.

[0027] The measurement control unit 215 controls the operation of the X-ray solution scattering apparatus 100. Control includes feeding the sample, generating X-rays, and moving the sample position and detector. Control instructions are transmitted to the control unit 140 within the X-ray solution scattering apparatus 100, thereby controlling various parts of the apparatus.

[0028] The measurement data storage unit 217 stores the measurement data of the X-ray solution scattering profile detected by the X-ray solution scattering device 100. The stored measurement data is used to generate electron density maps, calculate indices, and calculate measured values ​​of polymer molecular sizes.

[0029] The electron density map generation unit 221 generates multiple electron density maps from the measured X-ray scattering profile obtained by measuring the sample S0. Details of the electron density map generation will be described later.

[0030] From the obtained electron density maps, we can calculate the dynamic radius of rotation Rg(ind) of the electron density map representing the target molecule, and χ, an index indicating the degree of agreement between the measured data and the calculated scattering curve for each electron density map. 2 These can be calculated and plotted to create the first plot (see Figure 8 below). The dynamic radius of rotation Rg of the molecule is one example of a parameter representing molecular size, but other parameters representing molecular size may also be used.

[0031] The electron density map generation unit 221 preferably generates multiple electron density maps by changing the conditions if there is a trend in the distribution of the first plot. This allows for the attempt to regenerate an electron density map if none of the electron density maps are valid. The electron density map generation unit 221 can also generate multiple electron density maps based on conditions instructed by the user. This allows for the attempt to generate an electron density map by changing the conditions if none of the electron density maps are valid.

[0032] The electron density map generation unit 221 can generate multiple electron density maps one by one in an iterative process according to the settings. This allows for processing while verifying the validity of the electron density maps by minimizing unnecessary processing, and allocating necessary computational resources to the processing. Alternatively, the electron density map generation unit 221 may generate multiple electron density maps simultaneously in parallel processing according to the settings. This allows for the reproduction of highly valid electron density maps of biomolecules in a short time.

[0033] The index calculation unit 226 calculates an index that represents the degree of agreement between the calculated X-ray scattering profile obtained from each of the multiple electron density maps and the measured X-ray scattering profile. Specifically, it calculates a statistically processed index called χ. 2 While this is preferable, it is not particularly limited to any index that represents the degree of agreement with the X-ray scattering profile. 2 Other examples include parameters of the normal or Poisson distribution, and indices representing the degree of agreement between the structure factor obtained from experimental diffraction data and the structure factor based on electron density obtained from analysis, such as the R value, RMS value, and RMD value. 2 It can be calculated as follows:

[0034]

number

[0035] The correlation determination unit 231 creates a first plot by plotting the parameter representing the molecular size against the calculated index for each of the multiple electron density maps, and determines whether or not there is a correlation in the first plot. Preferably, the correlation determination unit 231 creates an outputtable first plot and displays the first plot on the display. This allows the user to visually confirm whether or not there is a correlation in the first plot.

[0036] When performing iterative processing, the correlation determination unit 231 preferably determines whether or not there is a correlation between the plots at each iteration. This allows the validity of the electron density map to be confirmed at each iteration as processing progresses. As a result, processing can be performed efficiently even when computing resources are limited.

[0037] The trend analysis unit 232 performs multivariate analysis on the distribution of the first plot if there is no correlation between the first plots. Examples of multivariate analysis include MCA (Multiple Correspondence Analysis) and PCA (Principal Component Analysis). This allows for the determination of the presence or absence of some kind of trend even if there is no correlation. For example, even if there is no correlation in the overall data, by separating multiple types of correlated data, each type of data can be used as correlated data.

[0038] The theoretical size calculation unit 245 creates a second plot for each voxel size by plotting parameters representing the molecular size calculated based on multiple electron density maps. The parameters representing the calculated molecular size include the χ² of the regression line of the calculated radius of gyration Rg(ind). 2 The intercept Rg(sect) at =1 is preferred. The theoretical size calculation unit 245 then uses the second plot to calculate the calculated value Rg(calc), a parameter representing the molecular size of the polymer in the solution, independent of the voxel size.

[0039] The measured size calculation unit 246 calculates parameters representing the molecular size of polymers in solution as measured values ​​from the measured X-ray scattering profile. Specifically, it can perform a Guinier plot and calculate the measured value Rg(exp) of the dynamic radius of rotation of the molecule. If the sample forms a hydration zone in the solution, a predetermined value for the hydration zone is calculated from the value obtained from the Guinier plot. added It is preferable to treat the numerical value as the measured value Rg(exp).

[0040] The comprehensive determination unit 257 determines whether there is a statistically significant difference between the calculated value Rg(calc) of the turning radius calculated by the theoretical size calculation unit 245 and the measured value Rg(exp) calculated by the measured size calculation unit 246. If it is determined that there is no significant difference, it prompts the unit to select a representative electron density map from among multiple electron density maps. If it is determined that there is a significant difference, the process is terminated.

[0041] The electron density map selection unit 258 selects a representative electron density map from a plurality of electron density maps based on the calculated index. Specifically, it selects a representative electron density map according to the Rg-χ² correlation of the obtained plurality of electron density maps, and χ² 2 An electron density map with a value close to 1 is selected as the representative electron density map. Because the representative electron density map is selected based on the index, the electron density map of polymers in solution with dynamically fluctuating structures can be accurately reproduced. As a result, even biomolecules in solution with no prior information can be accurately visualized.

[0042] The electron density map selection unit 258 preferably does not select a representative electron density map if there is no correlation in the first plot. This allows the identification of an electron density map to be stopped and unnecessary calculations to be avoided if none of the electron density maps are valid. Then, depending on the situation, the electron density map can be regenerated or the experiment can be repeated.

[0043] The electron density map selection unit 258 preferably does not select a representative electron density map if the difference between the calculated value and the measured value is not within a predetermined range. This allows the selection of an electron density map to be stopped even if an electron density map can be identified, if the validity of the electron density map cannot be guaranteed in terms of molecular size.

[0044] [Method for identifying electron density maps] (entire method) A method for identifying the electron density map of a polymer in a solution using the electron density map identification system 10 configured as described above will now be explained. Figure 4 is a flowchart showing the operation of the electron density map identification device 200. First, the X-ray solution scattering device 100 sends a solution containing the sample S0 to a predetermined position and irradiates the sample S0 with X-rays. The X-ray solution scattering device 100 detects the scattered X-rays and transmits them to the computer 210 as X-ray scattering profile data. The computer 210 stores the received X-ray scattering profile data.

[0045] The computer 210, upon receiving a user specification, reads the X-ray scattering profile data obtained from the sample S0 for which it intends to determine the electron density map (step S1). Then, it obtains the electron density map generation conditions, such as the boundary value size, voxel size, and the number of trials for each voxel size, as specified by the user (step S2).

[0046] Based on the acquired generation conditions, an electron density map is generated from the read-out X-ray scattering profile (Step S3). Details of the electron density map generation will be described later. Next, a theoretical scattering profile is calculated based on the generated electron density map (Step S4). Based on the read-out measured X-ray scattering profile and the calculated theoretical scattering profile, the calculated value Rg(ind) of the particle gyration radius of the target molecule for each electron density map and the index χ representing the degree of agreement between the calculated X-ray scattering profile based on the electron density map and the measured X-ray scattering profile are calculated. 2 Calculate (Step S5), χ 2 Create a plot of -Rg(ind) (step S6).

[0047] Next, as a repetition condition, it is determined whether the generation of the electron density map has been attempted a predetermined number of times for a specific voxel size (step S7). If it is determined that the attempt has not been made a predetermined number of times, the process returns to step S3. If it is determined that the attempt has been made a predetermined number of times, the process proceeds to step S8. The predetermined number of times is, for example, 50 times. In the above example, the repetitive process is performed for a specific voxel size in step S7, but the repetitive process may simply be performed a predetermined number of times.

[0048] In this way, it is determined whether there is a correlation with the plot of χ 2 -Rg(ind) created for a specific voxel size (step S8). Details of the correlation determination process will be described later. If it is determined that there is no correlation, it is determined whether there is any tendency in the plot by multivariate analysis (step S9). If it is determined that there is a tendency, the process returns to step S3, the conditions are changed, and the electron density map is created again. If it is determined that there is no tendency, the series of processes is terminated without selecting a representative of the electron density map. By determining the presence or absence of correlation at the stage when the repetitive process in step S7 ends and terminating the process with no prospect, computational resources can be used efficiently.

[0049] On the other hand, if it is determined in step S8 that there is a correlation, it is determined whether the condition for ending the repetition, that is, whether the generation of the electron density map has been completed for all of the plurality of voxel sizes, is satisfied (step S10). If it is determined that the condition is not satisfied, the voxel size is changed and the process returns to step S3.

[0050] In step S10, if the condition for ending the repetition is satisfied, a regression line is obtained from the plot of χ 2 -Rg(ind) according to the set of electron density maps, and the χ 2The intercept Rg(sect) at =1 is calculated (step S11). Then, a plot of the intercept Rg(sect) against the voxel size is created (step S12), a regression line is obtained from this plot, and the calculated value of the radius of gyration of the numerator Rg(calc) is calculated as the extrapolation value at which the voxel size is zero on the regression line (step S13). Meanwhile, a Guinier plot is created for the read X-ray scattering profile and the measured value of the radius of gyration of the numerator Rg(exp) is calculated (step S14).

[0051] Next, the calculation value Rg(calc) is determined to be valid by determining whether the difference between the calculated value Rg(calc) and the measured value Rg(exp) of the radius of rotation falls within a certain range (step S15). At this time, if the sample forms a hydration zone in the solution, a predetermined value for the hydration zone is obtained from the value obtained from the Guinier plot. added It is preferable to treat the numerical value as the measured value Rg(exp). When a hydration zone is formed, the predetermined value is preferably 1.5 Å to 2.0 Å. Alternatively, the size of the hydration zone estimated by various calculation methods, which are intended to explicitly calculate the existence of a hydration zone, may be used.

[0052] In step S15, if the calculated value Rg(calc) is not deemed valid, the series of processes is terminated without selecting a representative of the electron density map. If the calculated value Rg(calc) is deemed valid, the series of χ 2 From the electron density map following the Rg correlation, χ 2 A representative electron density map is selected from those closest to 1, and the selected electron density map is output to the output device 290 (step S16), thus ending the series of processes.

[0053] The representative electron density map is not necessarily limited to one; there may be multiple maps. For example, χ 2 -Rg(ind) plot shows a strong series of correlations, and χ 2If multiple electron density maps with values ​​very close to 1 are obtained, these may be selected as the electron density maps corresponding to each canonical structure of the dynamic structure ensemble. In this case, it is desirable to select from the correlation with the smallest voxel size. Alternatively, it is desirable to select the correlation defined with the smallest voxel size among the correlations generated with various voxel sizes.

[0054] In the example above, multiple electron density maps are generated in each iteration, but they could also be generated simultaneously using parallel processing. Alternatively, a fixed number of parallel processes could be repeated. The choice of processing method depends on whether computational resources or the speed of result generation are prioritized.

[0055] (Generating an electron density map) Next, we will explain the details of generating the electron density map. Figure 5 is a graph showing an example of an X-ray solution scattering profile. When X-rays are irradiated onto biomolecules in solution, q ≤ 0.7 Å -1 A gentle ring-shaped scattered X-ray intensity peak is generated within a certain range. By integrating these peaks in the circumferential direction, an X-ray solution scattering profile like the one shown in Figure 5 is obtained. In particular, the q range is 0.7 Å. -1 By acquiring and analyzing high-precision scattering intensity data up to that point, it becomes possible to directly visualize the electron density that is meaningful for the actual structure.

[0056] Figure 6 is a schematic diagram showing the electron density map. In generating the electron density map, the volume of a cube box with side length H in real space containing the polymer is first discretized into an N×N×N grid of voxels in the cube (N=4 in the example shown in Figure 6). As shown by the shading of each voxel in Figure 6, the electron density ρ(x,y,z) of each voxel is randomly assigned a value within a certain range. Then, the three-dimensional reciprocal lattice space intensity is calculated from the three-dimensional structure factor and divided into concentric shells as a function of the magnitude of the scattering vector q.

[0057] Then, the 3D scattering intensity is converted to a 1D profile and compared with the experimental scattering data. The 3D structure factor is scaled to match the experimental data for each concentric shell of q, and a new electron density map is created in real space by inverse Fourier transform. The density outside the map is set to zero. A new structure factor is obtained by forward Fourier transform, and this cycle is repeated until convergence occurs. In this way, a different electron density map is generated for each trial, and an index χ is given for each electron density map. 2 And the calculated value Rg(ind) is calculated.

[0058] (Correlation determination process) The χ calculated for each electron density map 2 By plotting Rg(ind) and determining whether they are correlated, the validity of the electron density map for the measured data can be assessed. Whether or not there is a correlation in the plots can be objectively determined, for example, by using the correlation coefficient. Furthermore, if there is no correlation, by determining whether or not there is a trend in the plots, it is possible to determine whether the data is unreliable or whether it could be meaningful depending on the measurement conditions.

[0059] Figures 7(a) and 7(b) show the ideal distribution and the unanalyzable χ², respectively. 2 This is a graph showing the -Rg(ind) distribution. In the ideal distribution shown in Figure 7(a), χ 2 A correlation appears in the -Rg(ind) plot, indicating that multiple electron density maps are valid. On the other hand, in the unanalyzable distribution shown in Figure 7(b), χ 2 The plot of -Rg(ind) shows no correlation or trend, indicating that multiple electron density maps are not valid. If the electron density map is valid, then χ 2 An electron density map in which the value falls within a predetermined range from 1 can be selected as a representative electron density map.

[0060] [Examples] We actually identified electron density maps using samples of biomolecules in solution (human serum albumin (HSA)). Electron density maps were generated through 50 trials for each voxel size of 10 Å, 5 Å, 4 Å, and 3 Å. Then, the χ² of the generated electron density maps was calculated. 2 And Rg(ind) was calculated. Figure 8 shows the index χ of the example. 2 This graph shows the distribution of the calculated radius of gyration of molecules, Rg(ind), for each of the following voxel sizes: 10 Å, 5 Å, 4 Å, and 3 Å. Correlations were confirmed for each of these voxel sizes.

[0061] Then, based on the straight line representing the correlation, Rg(sect) was calculated for voxel sizes of 10 Å, 5 Å, 4 Å, and 3 Å. Figure 9 is a graph showing the extrapolation of Rg(sect) to the voxel sizes of the example. By plotting the voxel size against the obtained Rg(sect), Rg(calc) for the entire set of electron density maps was calculated. From these results, it was found that the generated electron density maps are valid.

[0062] Figure 10 is a list showing the electron density map and processing results in the examples. A more reasonable electron density map can be obtained by reducing the voxel size, so for each trial with a voxel size of 3 Å, χ was calculated. 2 The values ​​were sorted in ascending order. According to the resulting list, χ 2 The electron density map from the 13th trial, where the difference from 1 was 0.002, was the most reasonable, and was therefore selected as the representative electron density map.

[0063] Figures 11(a) to 11(c) are front, top, and right side views, respectively, showing the selected electron density maps. As described above, we were able to identify and visualize the electron density map for the 13th trial run with a voxel size of 3 Å.

[0064] The visualized electron density exhibits a shape similar to that of a human liver overall. This closely represents the molecular surface shape obtained from X-ray crystallography of HSA. Furthermore, in Figure 11(a), a depression of approximately 5 Å and a cylindrical bulge along it are observed extending from the center of the longest side in the lower right to the upper left. Thus, the visualized shape, not only in terms of the overall shape but also in terms of the fine features of the molecular surface structure, closely matches the shape obtained from X-ray crystallography. [Explanation of symbols]

[0065] 10. Electron Density Map Identification System 100 X-ray solution scattering device 110 X-ray generation section 111 X-ray source 115 Optical system 117 Kratsky Block 120 Sample Loading Mechanism 125 Sample holding tube 130 detectors 140 Control Unit 200 Electron Density Map Identification Device 210 Computers 211 Input / Output Control Unit 215 Measurement Control Unit 217 Measurement data storage unit 221 Electron density map generation unit 225 Theoretical scattering intensity calculation section 226 Indicator calculation section 231 Correlation Determination Unit 232 Trend Analysis Department 245 Theoretical Size Calculation Unit 246 Actual Size Calculation Unit 257 Overall Judging Section 258 Electron Density Map Selection Section 280 Input devices 290 Output device L control bus

Claims

1. A device for calculating the radius of rotation of a polymer in a solution, An electron density map generation unit generates multiple electron density maps from the measured X-ray scattering profile obtained by measuring a sample, A gyroscopic radius calculation device comprising: a theoretical size calculation unit that creates a second plot of the dynamic gyroscopic radius of a molecule calculated based on the plurality of electron density maps for each of a plurality of voxel sizes, and calculates an extrapolated value where the voxel size is zero on the regression line of the second plot as the final calculated value of the dynamic gyroscopic radius of the molecule.

2. The system further includes an index calculation unit that calculates an index representing the degree of agreement between the calculated X-ray scattering profile calculated from each of the plurality of electron density maps and the measured X-ray scattering profile. The rotation radius calculation device according to claim 1, characterized in that the theoretical size calculation unit creates a second plot based on a first plot which is a plot of the dynamic rotation radius of a molecule against the calculated index created for each of the plurality of electron density maps.

3. The rotation radius calculation device according to claim 2, characterized in that for each of the multiple voxel sizes, the dynamic rotation radius of the molecule calculated based on the multiple electron density maps is the intercept in the first plot.

4. X-ray solution scattering apparatus, A turning radius calculation device according to any one of claims 1 to 3, comprising: The rotation radius calculation device is a system characterized by calculating the dynamic rotation radius of a polymer in a solution based on the X-ray scattering profile of the polymer in the solution measured by the X-ray solution scattering device.

5. A method for calculating the radius of rotation of a polymer in a solution, The steps include generating multiple electron density maps from the measured X-ray scattering profile obtained by measuring the sample, The steps include creating a plot of the dynamic radius of rotation of the molecule calculated based on the plurality of electron density maps for each of the plurality of voxel sizes, A method for calculating the radius of rotation, characterized by comprising the step of calculating an extrapolated value where the voxel size is zero on the regression line of the plot as the final calculated value of the dynamic radius of rotation of the numerator.

6. A program for calculating the radius of rotation of a polymer in a solution, A process to generate multiple electron density maps from the measured X-ray scattering profile obtained by measuring the sample, A process to create a plot of the dynamic radius of rotation of molecules calculated based on the multiple electron density maps for each of the multiple voxel sizes, A program for calculating the radius of rotation, characterized by causing a computer to perform the following steps: calculate the extrapolated value at which the voxel size becomes zero in the regression line of the plot as the final calculated value of the dynamic radius of rotation of the numerator.

Images