Main

Protoclusters are the earliest phase in the assembly of large-scale cosmic structures. These systems mark a transition from initial galaxy overdensities to fully virialized galaxy clusters. X-ray and Sunyaev–Zel’dovich (SZ) observations have been widely used to identify clusters and protoclusters in the early universe, up to z ≈ 2.5, that are either gravitationally collapsed or in the process of collapsing11,12,13,14,15,16,17,18,19. However, detecting protoclusters within the first billion years of the universe (z ≳ 5.5) remains a great challenge. At these early epochs, halos may not yet have experienced substantial virial heating (that is, shocks that bring the gas up to the virial temperature of the halo) or may only be in their earliest stages1,3. This makes observing the faint hot ICM, the key signature of the onset of virial heating, difficult. Therefore, identifying the first protoclusters undergoing virialization necessitates a multi-wavelength effort. Although overdensity measurements reveal dense galaxy environments, unambiguous confirmation of the onset of gravitational collapse comes from the detection of ICM20,21,22. In this work, we extend this approach by using JWST and Chandra data to investigate an even earlier protocluster, merely one billion years after the Big Bang.

JWST observations have revolutionized the study of high-redshift structures by identifying substantial populations of faint and distant galaxies23,24,25. Its near-infrared imaging capability and accurate photometric redshifts allow the identification of galaxy overdensities, paving the way for detecting the earliest protoclusters. In the JADES field26, one of JWST’s premiere regions, six protocluster candidates were identified in the redshift range z = 5–7 (ref. 8). Of these protoclusters, JADES-ID1 is the most compelling candidate, exhibiting high galaxy overdensity and cluster membership likelihood. A total of 66 galaxies are identified as potential members, with an inferred halo mass of (\log ({M}_{{\rm{h}}}/{M}_{\odot })=13.2{8}_{-0.34}^{+0.37}), the highest among the JADES fields8. Because only JADES-ID1 has the richness and halo mass to produce a detectable ICM signal in the JADES field, our X-ray analysis targets this protocluster candidate. The Chandra Deep Field South (CDFS)/JADES field uniquely combines deep JWST imaging with the deepest Chandra exposure over a single footprint, making it at present the only survey volume in which X-ray emission from the ICM of high-redshift protoclusters could, in principle, be detected. Further details on the identification of JADES-ID1 and quantitative tests ruling out the presence of projected foreground galaxy groups and clusters are presented in Methods section ‘JWST characterization of the JADES-ID1 protocluster’.

Within a projected radius of 42″ (≈250 kpc) around the JADES-ID1 centroid, we measure the local galaxy overdensity of δgal = 3.9 relative to the mean galaxy density across the JADES field at the same redshift slice8. In the inner 21″ (≈125 kpc) region (coinciding with the detected X-ray emission), the overdensity increases to δgal = 4.5. This corresponds to a 4.2σ overdensity detection (for details, see Methods section ‘JWST characterization of the JADES-ID1 protocluster’). At z ≈ 5.7, this overdensity is exceptionally rare. Above z >5 , the expected amplitude of galaxy overdensities falls off sharply owing to the declining galaxy number density, increasing photometric incompleteness and the fact that large-scale structure has had less time to collapse. Although the large galaxy overdensity associated with JADES-ID1 indicates a nascent protocluster, X-ray data can confirm whether the virialization has begun. Indeed, detecting hot ICM, best accomplished through sensitive X-ray imaging, can trace the gravitational potential of the protocluster and allows a more precise determination of its centroid, luminosity and total mass.

To examine the X-ray-emitting properties of JADES-ID1, we used deep Chandra Advanced CCD Imaging Spectrometer (ACIS-I) X-ray observations of the CDFS. The CDFS overlaps with the JADES field and is the site of the deepest X-ray observation ever conducted27,28. The data were analysed with CIAO tools29. First, the 99 individual observations (Extended Data Table 1) were reprocessed with the chandra_repro tool. These observations were then merged into a single event file, which had a total exposure time of 6.55 Ms. Next we generated images and their corresponding exposure maps in the 0.5–2.0-keV and 3–7-keV energy ranges. Bright X-ray point sources were excluded from the analysis. A complete description of the data analysis is presented in Methods section ‘Chandra data analysis’.

Figure 1 presents a multi-wavelength view of the JADES-ID1 protocluster and its surroundings. Although the JWST data reveal a galaxy overdensity at z ≈ 5.7, an initial inspection of the exposure-corrected 0.3–2.0-keV Chandra image does not show bright X-ray emission cospatial with JADES-ID1. It also indicates that none of the high-redshift galaxies are detected as individual X-ray point sources and a stack of the galaxy positions likewise shows no statistically significant signal (Methods section ‘Excluding alternative origins of the X-ray emission’). To better assess the presence of faint diffuse emission expected from a z ≈ 5.7 protocluster, we carry out an in-depth imaging analysis. To do this, we first filled the location of the excluded point sources using the dmfilth tool using the ‘global’ method. Next we subtracted the background components using an annulus with 40″–110″ radii around JADES-ID1 (Methods section ‘Chandra data analysis’). Finally, we applied Gaussian smoothing to the image with a kernel size of 15 pixels.

Fig. 1: Multi-wavelength view of the JADES-ID1 protocluster and its surroundings.

a, Composite JWST image of the JADES field with a 45″ × 45″ (265 × 265 kpc) box marking JADES-ID1. Scale bar, 30″. b, Zoom-in on that region. Scale bar, 10″. c, The exposure-corrected 0.3–2.0-keV band Chandra image of the same region. Scale bar, 10″. d, A JWST/Chandra overlay of JADES-ID1, in which the Chandra image has been processed by filling point sources, subtracting the background and applying Gaussian smoothing with a kernel size of 15 pixels. Scale bar, 10″, 59 kpc at z = 5.68. e, The same processed Chandra image, with the locations of likely cluster member galaxies highlighted. The Chandra image reveals extended X-ray emission that is spatially coincident with the galaxy overdensity identified by JWST. Scale bar, 10″.

The resulting image, shown in Fig. 1e, indicates that large-scale diffuse X-ray emission is present near the JWST-derived centroid. We find that the X-ray centroid (RA = 3 h 32 min 31.75 s, dec = −27° 46′ 51.5″) is offset by about 8″ (about 47 kpc) from the galaxy overdensity peak. Such separations are commonly observed in dynamically young or merging systems. Systematic studies of disturbed clusters find mean X-ray/optical offsets of about 75 kpc, with offsets reaching and exceeding roughly 100 kpc in the most unrelaxed cases30,31,32. Even high-redshift systems, which are still in the early stages of collapse or undergoing mergers, exhibit comparable offsets13,19. Furthermore, owing to the broad Gaussian smoothing kernel (15 Chandra pixels or 7.4″) applied to enhance faint emission, our X-ray centroid is uncertain at the few arcsecond level. The 0.3–2.0-keV Chandra image nonetheless clearly shows extended emission spatially coincident with the galaxy overdensity, suggesting the presence of a large-scale hot ICM. Motivated by the detection of extended emission, we quantify this emission through a multi-faceted approach: (1) we establish its extended nature by constructing a surface brightness profile; (2) we examine its presence in different X-ray energy ranges; and (3) we examine its spectral properties. We note that the unsmoothed, point-source-masked image was used for the further quantitative analysis.

To quantify the large-scale diffuse ICM emission associated with JADES-ID1, we constructed an exposure-corrected, azimuthally averaged surface brightness profile from the unsmoothed, point-source-masked 0.3–2.0-keV band Chandra image, centred on the X-ray centroid. The background was measured in an annulus with 40″–110″ (235–646 kpc at z = 5.68) radii. For the background subtraction, we accounted separately for vignetted (Milky Way foreground plus unresolved cosmic X-ray background) and non-vignetted (particle background) components by generating two exposure maps: one includes mirror vignetting and detector effects and the other only includes detector effects. We applied each map to its corresponding background components (see Methods section ‘Chandra data analysis’ for details). We also verified that the resulting surface brightness profile is insensitive to the exact choice of background region. The background-subtracted surface brightness profile, presented in Fig. 2, reveals extended X-ray emission within about 21″ (≈125 kpc) and a declining trend with radius from the centre. Beyond this radius, the signal-to-noise ratio declines and the emission becomes consistent with the background. Fitting this surface brightness profile with a β-model with fixed β = 0.6 yields a core radius of rc = 7.1″ ± 3.9″ (42 ± 23 kpc). The observed 0.3–2.0-keV band emission is much more extended than the Chandra point spread function (90% of the encircled is contained within 1″), confirming the truly extended nature of this emission.

Fig. 2: X-ray surface brightness profile of the JADES-ID1 protocluster.

The 0.3–2.0-keV band profile was extracted in concentric annuli centred on the X-ray peak. The dashed line shows the best-fit β-model. The profile is corrected for exposure variations using the exposure map. The background is subtracted on the basis of the 40″–110″ (235–646 kpc at z = 5.68) annulus around the protocluster. The resulting background level is 8.03 × 10−10 photons s−1 cm−2 arcsec−2. Extended emission is detected out to approximately 21″ (≈125 kpc). The error bars represent statistical uncertainties derived using the Gehrels approximation58.

Within a 21″ aperture (≈125 kpc) of the JWST-derived centroid, in which the signal-to-noise ratio peaks, we measure 142 ± 45 net counts and 1,858 background counts, supporting the detection of an extended ICM. If this emission originates from plasma with a few keV temperature, we do not expect to detect X-ray emission in the 3–7-keV band. Indeed, at z ≈ 5.68, the observed 3–7-keV band corresponds to the 20.0–46.8-keV band in the rest frame of the cluster, in which such thermal emission is negligible. In agreement with this, the 3–7-keV band surface brightness profile does not show statistically significant X-ray emission in the same aperture. We detect only 51 ± 55 net counts and 2,947 background counts, consistent with the interpretation that the detected 0.3–2.0-keV band emission originates from a hot ICM.

Because of the relatively low count rate and the limited signal-to-noise ratio, extracting and fitting an X-ray spectrum of JADES-ID1 is not feasible. Instead, we investigate the spectral properties of the diffuse X-ray emission by calculating an X-ray hardness ratio HR = S/H, in which S and H correspond to the counts in the 0.5–1.2-keV and 1.2–2.0-keV bands, respectively (for details, see Methods section ‘X-ray hardness ratios’). Within the same 21″ source region, we obtain ({\rm{HR}}=1.8{4}_{-1.84}^{+1.96}). Although the large uncertainties only allow a broad estimate, these values imply an ICM temperature of at least about 2.5 keV, consistent with a hot protocluster.

We next combine the key X-ray observables—the 0.3–2.0-keV band detection, the 3–7-keV band non-detection and the declining surface brightness profile—into a combined likelihood map. This map quantifies the likelihood of random fluctuation mimicking all of these observational signatures simultaneously. For details on this map, see Methods section ‘Detection significance map’. In this map, shown in Fig. 3, JADES-ID1 stands out as the highest likelihood detection. Specifically, we find that the combined likelihood of detecting a statistical fluctuation with these parameters is 2.6 × 10−7, which corresponds to a 5.0σ detection. Although a few other regions also show elevated values on this map, those may trace structures at lower redshifts or they could represent statistical fluctuations. Thus, we conclude that the detected diffuse emission most likely originates from hot ICM associated with the JADES-ID1 protocluster. Finally, we combine the JWST-based overdensity significance (≈4.2σ)8 and Chandra X-ray detection likelihood (≈5.0σ) to establish the overall confidence level for JADES-ID1. We thus obtain a joint P-value of 3.4 × 10−12, which corresponds to a 6.9σ detection.

Fig. 3: Combined detection likelihood of JADES-ID1 and its surroundings.

White contours show the 3–7-keV band emission. The map incorporates the probability of having a 0.3–2.0-keV band detection, a 3–7-keV band non-detection and a radially declining surface brightness profile. The position of the protocluster is highlighted with a magenta circle with 7″ radius. Scale bar, 1′ = 354 kpc.

On the basis of the detection of hot ICM associated with JADES-ID1, we derive the X-ray luminosity and total mass of the protocluster. For this, we use the net count rate within a 21″ radius, along with the Chandra exposure maps to calculate the X-ray flux. We assume an optically thin thermal plasma emission model with k**T = 2 keV temperature, Z = 0.3 Z⊙ metallicity33,34 and a galactic hydrogen column density of NH = 6.7 × 1019 cm−2 (ref. 35). This yields an absorption-corrected 0.3–2.0-keV band X-ray flux of fX = (4.6 ± 1.5) × 10−16 erg s−1 cm−2. Using the redshift of z = 5.68 and applying a bolometric correction, we obtain a bolometric (0.01–100 keV) luminosity of ({L}_{{\rm{bol}}}=(1.{5}_{-0.6}^{{+0.5})\times 1{0}}{44},{\rm{erg}},{{\rm{s}}}^{{-1}). To estimate the total mass and ICM temperature of the protocluster, we assume self-similar evolution and apply the Lbol–M500 and Lbol–k**T scaling relations obtained for ‘all clusters’ in the sample of ref. 36. These result in a gas temperature of (kT=2.{7}_{-0.7}}{+0.5},{\rm{keV}}), which is consistent with the lower limit from the analysis of the X-ray hardness ratio. Finally, on the basis of the luminosity, we estimate a total cluster mass of ({M}_{500}=(1.{8}_{-0.7}^{{+0.6})\times 1{0}}{13},{M}_{\odot }), which corresponds to R500,c ≈ 80 kpc at z = 5.68. We note that the uncertainties include the statistical errors on the flux measurements and the uncertainties on the scaling relation parameters. However, these estimates carry several caveats. First, the assumption of self-similar evolution may not fully capture deviations from the scaling relations at high redshift, in which protoclusters are still assembling and undergoing early-stage accretion. Second, if JADES-ID1 is experiencing mergers or shocks, its ICM temperature and luminosity could be elevated37,38,39,40,41,42. However, such merger-driven boosts only add a modest bias in the scaling relations and do not qualitatively alter our conclusions38,43,44. Third, if the ICM temperature or metallicity differs from the assumed values, it could introduce a small change in the inferred parameters, although it would not alter our conclusions in any notable way. Finally, deviations from hydrostatic equilibrium, which are expected in dynamically young systems, could also affect the mass estimates, as non-thermal pressure support from turbulence or bulk flows may bias the derived masses low45,46.

The JWST-Chandra detection of a protocluster and its hot ICM at z = 5.7 provides insights into the formation of the first galaxy clusters and constrains the evolution of the hot ICM. JADES-ID1 is a rare example of a protocluster caught in the early phases of virial heating34,47. Theoretical studies suggest that protocluster shock heating (virialization) typically begins at lower redshifts (z ≈ 2–3) (ref. 2). However, the presence of a hot ICM in JADES-ID1 demonstrates that, at least in some of the most massive protoclusters, this process began merely one billion years after the Big Bang. Although the detection of a hot ICM indicates the onset of gravitational collapse, the protocluster is unlikely to be fully virialized at this early stage. The signatures of ICM heating in JADES-ID1 may be linked to its exceptional richness. Indeed, with 66 potential members, it is by far the richest protocluster candidate in the sample of ref. 8, suggesting that its deep gravitational potential could have accelerated both its collapse and the heating of its ICM.

The detection of a massive protocluster with ({M}_{500}=(1.{8}_{-0.7}^{{+0.6})\times 1{0}}{13},{M}_{\odot }) at such a high redshift is rather surprising. This detection provides an important data point for examining the abundance of large-scale structure systems in the early universe. To quantify how rare such systems are, we used the Tinker halo mass function and derived the expected number of massive halos within the z = 5–7 redshift range10. At these redshifts, the observable universe is predicted to host only a few dozen systems with M500 = 1013 M⊙ and less than one with M500 = 2 × 1013 M⊙ mass. Considering the small volume examined by the JADES/CDFS field, with the Chandra pointings covering a footprint of 16′ × 16′ (or a comoving volume of about 1.3 × 106 Mpc3), the probability of detecting a 1013 M⊙ protocluster in this region is about 4 × 10−5 under a ΛCDM cosmology48. The probability drops even further to about 2 × 10−7 for a protocluster with a mass of 2 × 1013 M⊙. To further illustrate the improbability of ≳1013 M⊙ halo, we note that the most massive halo in our survey volume is expected to be about 1012 M⊙, roughly an order of magnitude below our X-ray-inferred mass. Although these halo abundance probabilities assume a cosmic average, the matter–density variance on the scales of the JADES field only modestly alters the detection likelihood (Methods section ‘JWST characterization of the JADES-ID1 protocluster’). Overall, the detection of the JADES-ID1 protocluster challenges our understanding of early-structure formation. This finding is analogous to recent JWST discoveries revealing an overabundance of unexpectedly luminous galaxies at z = 9–12 (refs. 23,24,49,50,51). However, we note that the presence of extended, shock-heated gas in an approximately 1013* M*⊙ halo is the direct consequence of gravitational collapse and virial shocks, offering a probe of rapid halo assembly. Taken together, these results provide further important clues that, in some regions, structure may have formed more rapidly than previously thought.

Continued multi-wavelength synergy is essential for mapping the first protoclusters. Although JWST identifies high-redshift galaxy overdensities, next-generation X-ray missions could detect their extended ICM52,53,54, whereas SZ experiments could reveal the thermal SZ imprint of the earliest protoclusters55,56,57.

Methods

JWST characterization of the JADES-ID1 protocluster

Here we overview several key aspects of the JWST analysis. Specifically, we summarize the method used to define the JADES-ID1 centroid, quantify the statistical significance of its galaxy overdensity and present tests that rule out the presence of any substantial low-redshift foreground structures.

To define the centre of JADES-ID1 (ref. 8), we construct two-dimensional galaxy overdensity maps in narrow-redshift slices using the DETECTIFz algorithm59, which uses Monte Carlo realizations of the redshift probability distribution function of each galaxy. We then identify the slice with the highest overdensity peak, z = 5.68 for JADES-ID1, and use the coordinates of that peak as the protocluster centre.

Next we quantify the rarity of the JWST-identified overdensity around JADES-ID1 by comparing it with field fluctuations. Within a projected radius of 42″ (≈250 kpc) around the JADES-ID1 centroid, the local galaxy overdensity is measured as δgal = 3.9 relative to the mean density across the JADES field in the same redshift slice8. Focusing on the inner 21″ (≈125 kpc) region, which is coincident with our X-ray aperture, the overdensity rises to δgal = 4.5. This is comparable with or exceeds those of previously confirmed protoclusters at similar redshifts7. To assess the statistical significance of this overdensity, we compared these values to the mean field density over 5.44 < z < 6.08 within a spherical volume of radius 410 kpc. Accounting for an approximately 30% cosmic variance, which is appropriate for the typical ultraviolet luminosities of candidate members8,60, we performed 106 Monte Carlo realizations. The chance of obtaining the observed overdensity of the observed galaxies by random fluctuation is 1.4 × 10−5, corresponding to a roughly 4.2σ detection. We note that our field baseline includes cluster members, so both δgal and its significance are slight underestimates relative to a purely field reference. This confirms that, at z ≈ 5.7, such a strong overdensity is exceptionally rare.

Although ref. 8 identifies a clear overdensity at z ≈ 5.68, we further verify that no other substantial structures exist at lower redshifts. To do this, we investigated the photometric galaxy catalogues based on JWST and Hubble Space Telescope (HST) observations in the JADES field. We measured the galaxy surface density within a 40″ × 40″ box centred on the X-ray emission peak, corresponding to the extent of the detected emission from the JADES-ID1 protocluster. We binned galaxies in redshift slices with width of Δz = 0.3 in the redshift range z = 0–6.6 and derived the surface density in each bin. To correct for redshift-dependent selection biases (most notably the increased completeness at lower redshifts), we carried out the same measurement in a large background region within the JADES footprint, while excluding the 40″ × 40″ region with the X-ray detection. The difference between the galaxy surface density at the position of the X-ray excess and the field average exhibits a single significant peak in the z = 5.25–6.23 redshift bin. There are no comparable galaxy overdensities at any other redshift bins. This result demonstrates the absence of any substantial foreground structure along the line of sight of the JADES-ID1 protocluster.

The halo detection probabilities presented in the main part of this paper are based on the cosmic mean density field. To estimate how local density fluctuations could bias these results, we estimate the variance of the matter density over a JADES-sized volume. We find σ(R) ≈ 0.059, which corresponds to a 6% typical fluctuation between different patches of this size. Although a 6% overdense field would allow structure to grow more rapidly, the chance of finding a 1013* M*⊙ halo would increase only from about 4 × 10−5 to about 3 × 10−4.

Chandra data analysis

To examine the presence and physical properties of the hot ICM associated with the protocluster JADES-ID1, we analysed 99 Chandra ACIS-I observations that cover the CDFS. The CDFS represents the deepest X-ray field ever observed. The list of analysed Chandra observations is given in Extended Data Table 1. We performed most of the data analysis using standard CIAO tools, specifically, we used the latest version of CIAO (4.17) and the Calibration Database (CALDB 4.11.6). The main steps of the X-ray data analysis followed those outlined in our previous studies61,62. Below, we outline the main steps of the X-ray analysis.

The first step of the analysis was to reprocess each individual observation using the chandra_repro tool, thereby applying the latest calibration products. Next we identified and filtered high-background periods from the observations using the lc_clean routine by applying a 3σ threshold to remove fluctuations in the light curves. Because ACIS-I observations are not highly sensitive to solar flares, this step only reduced the exposure time by approximately 2%. The total cleaned exposure time of the dataset was 6.55 Ms.

Because we analyse and combine a large set of observations, small differences exist in the alignment between the individual Chandra observations. To account for this effect, we correct the absolute astrometry using the wcs_match and wcs_update tools. This step ensures that point sources are accurately aligned and exhibit a sharp point spread function, thereby minimizing contamination of the extended emission. To perform the astrometry correction, we cross-matched the positions of X-ray point sources in individual observations with the coordinates of guide stars in the same field. Using the coordinates of the X-ray–optical source pairs, we applied frame transformations for each Chandra observation, including transformations for rotation, scale and translation. We set the deepest observation, ObsID 8594, as the reference coordinate system. For the subsequent analysis, we used these astrometry-corrected event files.

The next step in the analysis was to combine the individual X-ray observations. For this, we used the merge_obs tool, which coadded the data, resulting in a merged event file with 6.55 Ms exposure time. This process also generated energy-filtered images in the 0.3–2.0-keV (soft) and 3–7-keV (hard) bands. In our analysis, we use the 0.3–2.0-keV range as our soft band because it maximizes sensitivity to a few-keV thermal plasma at z ≈ 5.7. Because most observations were taken relatively early in the Chandra mission, molecular contamination is minimal63,64, allowing us to extend reliably down to 0.3 keV. For the hard band, we use the 3–7-keV band, thereby avoiding the 2–3-keV energy range in which the Au L fluorescence line complex dominates65,66. This hard band is sensitive to unresolved active galactic nuclei (AGN), very hot ICM at high redshift or ICM emission from nearby clusters. We generated exposure maps for both energy ranges using this tool. These maps account for vignetting, molecular contamination, gaps between charge-coupled devices and the filtering of bad pixels. To construct the exposure maps, we assumed an optically thin thermal plasma model (APEC in XSPEC) with a galactic column density of NH = 6.8 × 1019 cm−2, a k**T = 2 keV temperature and Z = 0.3 Z⊙ solar abundance. The count images were then divided by the exposure maps, producing the exposure-corrected images used in the analysis.

To study the extended emission associated with JADES-ID1, we must ensure that bright X-ray point sources do not contaminate the extended emission from the protocluster. Therefore, we searched for resolved X-ray point sources (mostly originating from the cosmic X-ray background) using the wavdetect tool. We searched for sources using the wavelet scales of 1.0, 1.414, 2.0, 2.828, 4.0, 5.657 and 8.0, which allows the detection of sources on a wide range of spatial scales and a significance threshold of 10−6. Furthermore, we set the ellsigma parameter to 5. To carry out a comprehensive masking of all point sources, we cross-referenced our source list with the CDFS point source list presented in ref. 28. We found that some of their faintest sources, detected using a lower significance threshold, fell below our initial detection criteria, so we added these to our point source catalogue. We then visually inspected the source regions and, for especially bright sources, enlarged the exclusion regions to fully encompass their point spread function wings. We note that, within the inner 21″ of JADES-ID1, only one moderately bright and two faint point sources are detected (Extended Data Fig. 1). The detected point source regions were excluded from the merged images. Given the sharp Chandra point spread function, our large exclusion regions account for ≳96% of the counts from each point source, implying that any residual counts have a negligible impact on the detected diffuse emission. Moreover, because spillover counts from point sources contribute similarly to both the source and the background regions, it does not bias our measurements in any notable way.

Because the X-ray emission from JADES-ID1 is relatively faint, precisely accounting for the background components is essential. The Chandra background comprises several components: the vignetted sky emission (Milky Way foreground and unresolved cosmic X-ray background) and the non-vignetted particle background. To separate these components, we generated two sets of exposure maps. One of them is a ‘full’ map including mirror vignetting and all ACIS detector corrections, whereas the other is a ‘detector-only’ map that does not include the vignetting term. We then split the total background accordingly and applied the full map to the sky component and the detector-only map to the particle component. In the deep CDFS field, Chandra resolves about 90% of the cosmic X-ray background, so we find that particle background accounts for about 77% of the 0.3–2.0-keV band and about 95% of the 3–7-keV band background.

To verify that the X-ray detection associated with JADES-ID1 is not driven by a small subset of observations, we split the CDFS Chandra data into two groups in two complementary ways. First, we divided the observations chronologically into two sets with approximately equal total exposure times. Owing to the build-up of the molecular contaminant on the ACIS optical blocking filter (which absorbs soft X-rays63,64) and the soft, redshifted spectrum of the JADES-ID1 protocluster, the earlier dataset contains approximately 65% of the net counts, whereas the later one includes about 35%. Second, we randomly split the observations into two groups once again with approximately equal exposure times. In this case, as both subsets have the same average molecular contamination level, the net counts split roughly evenly between them. These tests demonstrate that the detected X-ray signal is not driven by a handful of observations or by temporal variation but arises uniformly across the Chandra dataset. This supports the conclusion that the X-ray emission associated with JADES-ID1 originates from a genuine, extended ICM.

X-ray hardness ratios

Owing to the relatively low number of net X-ray counts and the limited signal-to-noise ratios associated with the JADES-ID1 protocluster, it is not feasible to fit a full X-ray