How to parse string to struct?

If you are still struggling with the separation of your input into flags, rate & timestamp, then the suggestions in the comments regarding using an unsigned type to hold your input string converted to a value, and using the exact width types provided in <stdint.h>, will avoid potential problems inherent in manipulating signed types (e.g. potential sign-extension, etc.)

If you want to separate the values and coordinate those in struct, that is 100% fine. The work come in separating the individual flags, rate & timestamp. How you choose to store them so they are convenient within your code is up to you. A simple struct utilizing exact-width type could be:

typedef struct {    /* struct holding sensor data */
    uint8_t  flags;
    uint16_t rate;
    uint32_t tstamp;   
} sensor_t;

In a conversion from char * to uint64_t with strtoull, you have two primary validation checks:

1. utilize both the pointer to the string to convert and the endptr parameter to validate that digits were in fact converted (strtoull sets endptr to point 1-character after the last digit converted). You use this to compare endptr with the original pointer for the data converted to confirm that a conversion took place (if no digits were converted the original pointer and endptr will be the same and the value returned will be zero); and

2. you set errno = 0; before the conversion and then check again after the conversion to insure no error occurred during the conversion itself. If strtoull encounters an error, value exceeds range, etc.., errno is set to a positive value.

3. (and if you have specific range validations, e.g. you want to store the result in a size less than that of the conversion, like uint32_t instead of uint64_t, you need to validate the final value can be stored in the smaller type)

A simple approach would be:

    uint64_t data = 0;                  /* exact width type for conversion */
    ...
    char *p = argc > 1 ? argv[1] : "0x5ABBF13A000A01",  /* input */
        *endptr = p;                    /* endptr for strtoul validation */
    errno = 0;          /* reset errno */
    ...
    data = strtoull (p, &endptr, 0);    /* convert input to uint64_t */

    if (p == endptr && data == 0) {     /* validate digits converted */
        fprintf (stderr, "error: no digits converted.\n");
        return 1;
    }
    if (errno) {    /* validate no error occurred during conversion */
        fprintf (stderr, "error: conversion failure.\n");
        return 1;
    }
    printf ("data: 0x%" PRIx64 "\n\n", data); /* output conerted string */

Finally, separating the value in data into the individual values of flags, rate & timestamp, can be done with simple shifts & ANDS, e.g.

    sensor_t sensor = { .flags = 0 };   /* declare instance of sensor */
    ...
    sensor.flags = data & 0xFF;                             /* set flags */
    sensor.rate = (data >> CHAR_BIT) & 0xFFFF;              /* set rate */
    sensor.tstamp = (data >> (3 * CHAR_BIT)) & 0xFFFFFFFF;  /* set timestamp */

    /* output sensor struct */
    printf ("sensor.flags : 0x%02" PRIx8 "\nsensor.rate  : 0x%04" PRIx16
            "\nsensor.tstamp: 0x%08" PRIx32 "\n", sensor.flags, sensor.rate,
            sensor.tstamp);

Putting it altogether, you could do something similar to:

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <stdint.h>
#include <inttypes.h>
#include <errno.h>
#include <limits.h>

typedef struct {    /* struct holding sensor data */
    uint8_t  flags;
    uint16_t rate;
    uint32_t tstamp;   
} sensor_t;

int main (int argc, char **argv) {

    uint64_t data = 0;                  /* exact width type for conversion */
    sensor_t sensor = { .flags = 0 };   /* declare instace of sensor */
    char *p = argc > 1 ? argv[1] : "0x5ABBF13A000A01",  /* input */
        *endptr = p;                    /* endptr for strtoul validation */
    errno = 0;          /* reset errno */

    data = strtoull (p, &endptr, 0);    /* convert input to uint64_t */

    if (p == endptr && data == 0) {     /* validate digits converted */
        fprintf (stderr, "error: no digits converted.\n");
        return 1;
    }
    if (errno) {    /* validate no error occurred during conversion */
        fprintf (stderr, "error: conversion failure.\n");
        return 1;
    }
    printf ("data: 0x%" PRIx64 "\n\n", data); /* output conerted string */

    sensor.flags = data & 0xFF;                             /* set flags */
    sensor.rate = (data >> CHAR_BIT) & 0xFFFF;              /* set rate */
    sensor.tstamp = (data >> (3 * CHAR_BIT)) & 0xFFFFFFFF;  /* set timestamp */

    /* output sensor struct */
    printf ("sensor.flags : 0x%02" PRIx8 "\nsensor.rate  : 0x%04" PRIx16
            "\nsensor.tstamp: 0x%08" PRIx32 "\n", sensor.flags, sensor.rate,
            sensor.tstamp);

    return 0;
}

Example Use/Output

$ ./bin/struct_sensor_bitwise
data: 0x5abbf13a000a01

sensor.flags : 0x01
sensor.rate  : 0x000a
sensor.tstamp: 0x5abbf13a

Look things over and let me know if you have further questions.