mx/Jungfraujoch
2
1
Fork 0
Code Issues Pull Requests 1 Actions 3 Packages Projects Releases 72 Wiki Activity

docs: add the eight new public datasets to the non-SLS test list

Browse Source 
Three IUCrData Raw Data Letters (Zenodo, CC-BY-4.0) and five SBGrid Data
Bank depositions (CC0) have been added to the data the pipeline is
exercised on. Same rules as the rest of the page: the source is the
repository and its own citable DOI, every one of which was resolved before
it was written down; beamline, resolution, space group and cell are the
values deposited with the PDB entry; the detector is read out of the image
files. None of the new detectors disagree with their PDB entry.

Two of them do not fit the page's one-row-per-sweep shape, so the shape is
described rather than flattened. The 6R72 Zenodo record holds two complete
360-degree collections on one crystal - a helical one that produced the
deposited structure and a low-dose one that has no PDB entry - and both are
listed, sharing a DOI, with the second in the no-PDB-entry table. The three
CHESS depositions are 4-11 wedges of 50 degrees per crystal plus a rotation
taken with the crystal translated out of the beam, tabulated in a new
section.

One SBGrid deposition is named but not in the table: its images are 1995 CCD
TIFFs, a format the reader does not support, so it is not processed here and
saying so is more useful than leaving it out.

ACKNOWLEDGEMENT gains the new per-repository counts and a pointer to the
Raw Data Letter citations; TESTS points at the page.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01T3yNBXk4wKdMZy1ak2NY7f
This commit is contained in:
leonarski_f
2026-08-29 23:40:10 +02:00
co-authored by Claude Opus 5
parent 08f57235d6
commit bec2a10a3a
3 changed files with 79 additions and 11 deletions
Download Patch File Download Diff File Expand all files Collapse all files
docs/ACKNOWLEDGEMENT.md
+5 -3
View File
@@ -43,14 +43,16 @@ Integrated Resource for Reproducibility in Macromolecular Crystallography: Exper
four years" (2019), Struct. Dyn. 6, 064301
[doi:10.1063/1.5128672](https://doi.org/10.1063/1.5128672).
**[SBGrid Data Bank](https://data.sbgrid.org/)** supplied five of the datasets. P. A. Meyer,
**[SBGrid Data Bank](https://data.sbgrid.org/)** supplied nine of the datasets. P. A. Meyer,
S. Socias, J. Key, E. Ransey, E. C. Tjon, A. Buschiazzo et al., "Data publication with the
structural biology data grid supports live analysis" (2016), Nat. Commun. 7, 10882
[doi:10.1038/ncomms10882](https://doi.org/10.1038/ncomms10882).
**[Zenodo](https://zenodo.org/)** hosts seven, deposited there directly by the groups that
**[Zenodo](https://zenodo.org/)** hosts eleven, deposited there directly by the groups that
collected them. European Organization for Nuclear Research and OpenAIRE, "Zenodo" (2013), CERN
[doi:10.25495/7GXK-RD71](https://doi.org/10.25495/7GXK-RD71).
[doi:10.25495/7GXK-RD71](https://doi.org/10.25495/7GXK-RD71). Three of those datasets were
published as IUCrData Raw Data Letters; the letters are cited on the
[NON_SLS_TEST_DATA](NON_SLS_TEST_DATA.md) page, beside the datasets they describe.
The beamline, resolution, space group and unit cell quoted for each dataset are the values
deposited with the corresponding PDB entry, read from the RCSB PDB data API. H. M. Berman,
docs/NON_SLS_TEST_DATA.md
+72 -7
View File
@@ -30,10 +30,15 @@ the table below; the repositories themselves are cited in
| PDB | Source | Facility / beamline | d<sub>min</sub> (Å) | Space group | Unit cell a b c α β γ (Å, °) | Detector (from file) | Title |
|---|---|---|---|---|---|---|---|
| [11IF](https://www.rcsb.org/structure/11IF) | IRRMC [10.18430/M311IF](https://doi.org/10.18430/M311IF) | NSLS-II 19-ID | 1.51 | P 43 | 51.1 51.1 71.9 90.0 90.0 90.0 | Dectris EIGER2 Si 9M | Crystal Structure of an exported phospholipid binding protein from Bordetella pertussis in complex with Di-palmitoyl-3-sn-phosphatidylethanolamine (DPPE), P43 form 2 |
| [5F6M](https://www.rcsb.org/structure/5F6M) | SBGrid [10.15785/sbgrid/201](https://doi.org/10.15785/sbgrid/201) | SSRL BL11-1 | 1.10 | P 21 21 21 | 54.8 58.5 67.4 90.0 90.0 90.0 | PILATUS 6M | Isotropic Trypsin Model for Comparison of Diffuse Scattering |
| [5REO](https://www.rcsb.org/structure/5REO) | Zenodo [10.5281/zenodo.3730956](https://doi.org/10.5281/zenodo.3730956) | Diamond I04-1 | 1.88 | C 1 2 1 | 112.4 52.6 44.4 90.0 103.0 90.0 | PILATUS 6M-F | PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102578 |
| [5SRC](https://www.rcsb.org/structure/5SRC) | IRRMC [10.18430/M35SRC](https://doi.org/10.18430/M35SRC) | ALS 8.3.1 | 1.05 | P 43 | 88.7 88.7 39.2 90.0 90.0 90.0 | PILATUS3 6M | PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5198562500 - (R,R) and (R,S) isomers |
| [6JGJ](https://www.rcsb.org/structure/6JGJ) | IRRMC [10.18430/m36jgj](https://doi.org/10.18430/m36jgj) | SPring-8 BL41XU | 0.77 | P 21 21 21 | 50.9 62.3 68.8 90.0 90.0 90.0 | PILATUS3 300K | Crystal structure of the F99S/M153T/V163A/E222Q variant of GFP at 0.78 A |
| [6LEO](https://www.rcsb.org/structure/6LEO) | Zenodo [10.5281/zenodo.4003042](https://doi.org/10.5281/zenodo.4003042) | SPring-8 BL32XU | 2.52 | C 2 2 21 | 73.5 95.3 101.4 90.0 90.0 90.0 | Dectris Eiger 9M | Crystal structure of thiosulfate transporter YeeE from Spirochaeta thermophila |
| [6O2H](https://www.rcsb.org/structure/6O2H) | SBGrid [10.15785/sbgrid/747](https://doi.org/10.15785/sbgrid/747) | CHESS F1 | 1.21 | P 1 | 27.4 32.1 34.5 88.7 108.5 111.9 | PILATUS3 6M | Hen lysozyme in triclinic space group at ambient temperature - diffuse scattering dataset |
| [6R72](https://www.rcsb.org/structure/6R72) | Zenodo [10.5281/zenodo.14894181](https://doi.org/10.5281/zenodo.14894181) | SOLEIL PROXIMA 2 | 3.95 | P 1 21 1 | 117.8 110.8 155.6 90.0 93.2 90.0 | Dectris Eiger 9M | Crystal structure of BmrA-E504A in an outward-facing conformation |
| — | Zenodo [10.5281/zenodo.14894181](https://doi.org/10.5281/zenodo.14894181) | | | | | Dectris Eiger 9M | Dataset for PDB 6r72 Crystal structure of BmrA-E504A in an outward-facing conformation |
| [6RLR](https://www.rcsb.org/structure/6RLR) | Zenodo [10.5281/zenodo.5886687](https://doi.org/10.5281/zenodo.5886687) | Diamond I04 | 2.00 | P 1 | 40.0 40.0 63.6 80.4 76.3 68.2 | Eiger 16M | Crystal structure of CD9 large extracellular loop |
| [6TTN](https://www.rcsb.org/structure/6TTN) | IRRMC [10.18430/m36ttn](https://doi.org/10.18430/m36ttn) | BESSY 14.1 | 1.12 | P 21 21 21 | 39.9 79.8 104.7 90.0 90.0 90.0 | PILATUS 6M | N-terminally truncated hyoscyamine 6-hydroxylase (tH6H) in complex with N-oxalylglycine and hyoscyamine |
| [6YQF](https://www.rcsb.org/structure/6YQF) | IRRMC [10.18430/m36yqf](https://doi.org/10.18430/m36yqf) | Diamond I24 | 3.33 | P 21 21 2 | 42.7 59.7 156.5 90.0 90.0 90.0 | PILATUS3 6M | Crystal structure of the SYCE2-TEX12 delta-Ctip complex in a 4:4 assembly |
| [6ZE4](https://www.rcsb.org/structure/6ZE4) | SBGrid [10.15785/sbgrid/806](https://doi.org/10.15785/sbgrid/806) | BESSY 14.1 | 1.60 | P 21 21 21 | 93.6 109.9 116.1 90.0 90.0 90.0 | PILATUS 6M | FAD-dependent oxidoreductase from Chaetomium thermophilum in complex with fragment 4-oxo-N-[(1S)-1-(pyridin-3-yl)ethyl]-4-(thiophen-2-yl)butanamide |
@@ -47,8 +52,11 @@ the table below; the repositories themselves are cited in
| [7QIS](https://www.rcsb.org/structure/7QIS) | IRRMC [10.18430/M37QIS](https://doi.org/10.18430/M37QIS) | BESSY 14.2 | 1.83 | P 61 | 100.3 100.3 206.2 90.0 90.0 120.0 | PILATUS3 2M | CRYSTAL STRUCTURE OF THE P1 difluoroethylglycine (DfeGly) BPTI MUTANT- BOVINE CHYMOTRYPSIN COMPLEX |
| [7RJI](https://www.rcsb.org/structure/7RJI) | IRRMC [10.18430/M37RJI](https://doi.org/10.18430/M37RJI) | LNLS W01B-MX2 | 1.71 | H 3 2 | 83.0 83.0 124.8 90.0 90.0 120.0 | PILATUS 2M | BthTX-II variant b, from Bothrops jararacussu venom, complexed with stearic acid |
| [7YZX](https://www.rcsb.org/structure/7YZX) | IRRMC [10.18430/M37YZX](https://doi.org/10.18430/M37YZX) | Diamond I24 | 1.90 | P 63 2 2 | 169.4 169.4 141.8 90.0 90.0 120.0 | PILATUS3 6M | ScpA from Streptococcus pyogenes, D783A mutant. |
| [8DYZ](https://www.rcsb.org/structure/8DYZ) | SBGrid [10.15785/sbgrid/957](https://doi.org/10.15785/sbgrid/957) | CHESS F1 | 1.27 | P 43 21 2 | 79.6 79.6 38.3 90.0 90.0 90.0 | PILATUS3 6M | Hen lysozyme in tetragonal space group at ambient temperature - diffuse scattering dataset |
| [8DZ7](https://www.rcsb.org/structure/8DZ7) | SBGrid [10.15785/sbgrid/958](https://doi.org/10.15785/sbgrid/958) | CHESS F1 | 1.34 | P 21 21 21 | 30.5 56.4 73.9 90.0 90.0 90.0 | PILATUS3 6M | Hen lysozyme in orthorhombic space group at ambient temperature - diffuse scattering dataset |
| [8EGN](https://www.rcsb.org/structure/8EGN) | IRRMC [10.18430/M38EGN](https://doi.org/10.18430/M38EGN) | CLSI 08B1-1 | 1.95 | P 21 21 21 | 71.7 75.2 109.8 90.0 90.0 90.0 | PILATUS3 6M | Crystal Structure of UDP-N-acetylmuramate-L-alanine ligase (UDP-N-acetylmuramoyl-L-alanine synthetase, MurC) Pseudomonas aeruginosa in complex with ligand AZ-13643701 |
| [8K1G](https://www.rcsb.org/structure/8K1G) | IRRMC [10.18430/M38K1G](https://doi.org/10.18430/M38K1G) | PAL/PLS 11C | 2.09 | I 4 2 2 | 182.0 182.0 80.7 90.0 90.0 90.0 | PILATUS3 6M | Crystal structure of ethylene glycol-bound glycerol dehydrogenase from Klebsiella pneumoniae |
| [8QQ7](https://www.rcsb.org/structure/8QQ7) | Zenodo [10.5281/zenodo.14901515](https://doi.org/10.5281/zenodo.14901515) | ESRF MASSIF-1 | 3.62 | P 64 2 2 | 146.0 146.0 153.6 90.0 90.0 120.0 | PILATUS3 2M | Structure of SpNOX: a Bacterial NADPH oxidase |
| [8R5R](https://www.rcsb.org/structure/8R5R) | IRRMC [10.18430/m38r5r](https://doi.org/10.18430/m38r5r) | ESRF ID23-1 | 3.08 | P 21 21 21 | 91.7 132.9 137.5 90.0 90.0 90.0 | Dectris EIGER2 CdTe 16M | Structure of apo TDO with a bound inhibitor |
| [8SA8](https://www.rcsb.org/structure/8SA8) | IRRMC [10.18430/M38SA8](https://doi.org/10.18430/M38SA8) | NSLS-II 19-ID | 1.30 | I 1 2 1 | 87.9 131.5 165.4 90.0 104.5 90.0 | Dectris EIGER2 Si 9M | Crystal Structure of Cystathionine beta lyase from Klebsiella aerogenes, Covalently bound and free PLP (I2 form) |
| [8SQQ](https://www.rcsb.org/structure/8SQQ) | IRRMC [10.18430/M38SQQ](https://doi.org/10.18430/M38SQQ) | NSLS-II 19-ID | 2.25 | F 4 3 2 | 171.5 171.5 171.5 90.0 90.0 90.0 | Dectris EIGER2 Si 9M | Crystal Structure of Bacterioferritin (Bfr) from Brucella abortus (Apo Cubic Form 2, F16L mutant) |
@@ -81,15 +89,71 @@ the table below; the repositories themselves are cited in
| — | Zenodo [10.5281/zenodo.20135265](https://doi.org/10.5281/zenodo.20135265) | Diamond Light Source I19-2 | | | | Eiger 2X 4M (CdTe) | Single-crystal X-ray diffractometry data for a sample of metformin collected on beamline I19-2 at Diamond Light Source with an Eiger 2X 4M with CdTe sensor |
| — | Zenodo [10.5281/zenodo.20041091](https://doi.org/10.5281/zenodo.20041091) | Diamond Light Source I19-2 | | | | Eiger 2X 4M (CdTe) | Single-crystal X-ray diffractometry data for a sample of Ni(dppe)Cl₂ collected on beamline I19-2 at Diamond Light Source with an Eiger 2X 4M with CdTe sensor |
The last rows have no PDB code. Four are small-molecule / chemical-crystallography datasets,
kept because they exercise short wavelengths, CdTe sensors and fine slicing; one is a protein
dataset whose IRRMC record names no PDB entry. They have no deposited macromolecular values,
so those columns are blank, and their titles are the repository record titles verbatim.
Six rows have no PDB code. Four are small-molecule / chemical-crystallography datasets, kept
because they exercise short wavelengths, CdTe sensors and fine slicing; one is a protein dataset
whose IRRMC record names no PDB entry; and one is the second collection in the 6R72 Zenodo
record, described below. They have no deposited macromolecular values, so those columns are
blank, and their titles are the repository record titles verbatim.
## Archives that are not a single sweep
Most rows above are a single continuous rotation. Four archives are not; their layout is read
from the image files, the repository file listings and the depositors' own description of the
record.
**6R72 - two collections on one crystal.** The Zenodo record holds two complete 360° sweeps of
3600 × 0.1° frames taken from the same crystal: a helical collection, which produced the
deposited structure, and a low-dose collection from a single position, which was not used for a
deposition and therefore has no PDB entry. Both are in the table, sharing one DOI; the deposited
values belong to the helical collection only. The record also ships the authors' `XDS.INP`.
**The three CHESS depositions - wedges plus a measured background.** Each crystal was rotated in
50° wedges of 500 × 0.1° frames and translated between wedges to spread the dose. Each crystal
also has a rotation at 1° per frame taken with the crystal translated out of the beam, which the
depositors include as a measured background and say can be matched to the diffraction frames by
the `phi` value in the image header.
| PDB | Crystals | Wedges per crystal | Background rotation |
|---|---|---|---|
| 8DYZ | 1 | 8 | 360 frames |
| 8DZ7 | 2 | 4 | 200 frames per crystal |
| 6O2H | 4 | 1, 3, 2, 5 - 11 in all | 50, 145, 95, 235 frames, one per crystal |
## Datasets published as Raw Data Letters
Three of the datasets - 6R72, 8QQ7 and 6RLR - were published as IUCrData Raw Data Letters, a
format whose purpose is to make raw images citable and re-processable in their own right. The
letters describe the collections and the difficulties in them, and are the reference for what the
data are:
- V. Zampieri, A. Vermot, M. Thepaut, I. Petit-Hartlein, F. Fieschi, P. Falson and V. Chaptal,
"X-ray diffraction images for two membrane protein crystals presenting high anisotropy; the
*B. subtilis* ABC transporter BmrA and the *S. pneumoniae* NADPH oxidase" (2025), IUCrData 10,
x250591 [doi:10.1107/S2414314625005917](https://doi.org/10.1107/S2414314625005917) - covers
6R72 and 8QQ7.
- V. Neviani, M. Lutz, W. Oosterheert, P. Gros and L. Kroon-Batenburg, "Crystal structure of the
second extracellular domain of human tetraspanin CD9: twinning and diffuse scattering" (2022),
IUCrData 7, x220852
[doi:10.1107/S2414314622008525](https://doi.org/10.1107/S2414314622008525) - covers 6RLR.
The authors of the second letter also published their own reciprocal-space reconstruction of the
6RLR data as a separate Zenodo record,
[10.5281/zenodo.6961763](https://doi.org/10.5281/zenodo.6961763).
## Obtained but not in the table
One further deposition was downloaded and is not listed above: SBGrid
[10.15785/sbgrid/1295](https://doi.org/10.15785/sbgrid/1295), the room-temperature Bragg and
diffuse-scattering data behind [4WOR](https://www.rcsb.org/structure/4WOR), collected at CHESS A1
in 1995. The images are stored as CCD TIFFs written by the detector software of the time, a
format the reader does not support, so the dataset is not processed here and the detector could
not be read from its images. It is named because the data are public and the deposition deserves
the same credit as the rest.
## Detector: image file vs PDB entry
For 45 datasets both the image file and the PDB entry name a detector that can be read as a
(model, generation, size). **12 of those 45 disagree** - 3 on the model or the size, and 9
For 52 datasets both the image file and the PDB entry name a detector that can be read as a
(model, generation, size). **12 of those 52 disagree** - 3 on the model or the size, and 9
only because the PDB entry omits the detector generation. The table above uses the file value
in every case.
@@ -112,7 +176,7 @@ The detector could not be read from the file for 8XTG (header reads `PILATUS XXX
## Deposited models and structure factors
46 of the 51 datasets have a released PDB entry, and RCSB reports released structure factors
53 of the 59 datasets have a released PDB entry, and RCSB reports released structure factors
(`status_code_sf = REL`) for all of them. A merged result from this pipeline can therefore be checked
against the deposited model or against the deposited intensities.
@@ -120,6 +184,7 @@ against the deposited model or against the deposited intensities.
| Dataset | Repository record | Why there is no PDB code |
|---|---|---|
| `6r72/ld` | Zenodo record 10.5281/zenodo.14894181, file prefix `V-CK63-8-ld_1_` | a second collection in the 6R72 record - a low-dose sweep on the same crystal, not the one the deposited structure was built from |
| `8agq` | IRRMC project page Phyco_JCSG_a3 | IRRMC's own project record for this archive names no PDB entry |
| `cuhf2` | Zenodo record 10.5281/zenodo.6347466 | a small-molecule dataset, not a PDB deposition |
| `dnba` | Zenodo record 10.5281/zenodo.1036416 | a small-molecule dataset, not a PDB deposition |
docs/TESTS.md
+2 -1
View File
@@ -35,7 +35,8 @@ exact commands; the CrystFEL fixtures are run by hand rather than in the pipelin
Two harnesses in the repository root run `rugnux` over a directory of stored datasets and score
the result. Neither is part of CI - run them when a change plausibly moves merged results, not as
a reflex. Both take their dataset list from **outside** the repository, because dataset and sample
identities are not committed.
identities are not committed. The public datasets the pipeline is exercised on, and the DOI to
cite for each, are listed in [Non-SLS test data](NON_SLS_TEST_DATA.md).
* `rugnux_vs_xds.py` - the rotation battery. Runs rugnux de novo over every crystal under a data
root and tabulates reflections, observations, space group, R_meas, CC1/2, ISa and wall-clock