From d8a3c6ea1573e5139b113ebc8c8d0cc8ba1785e5 Mon Sep 17 00:00:00 2001 From: Filip Leonarski Date: Fri, 9 Oct 2026 20:31:28 +0200 Subject: [PATCH] battery: add five large-cell sets to the open arm 4MTK (P61, c 653 A, PILATUS 6M miniCBF, SBGrid 235), 4NWV (I222 virus-like particle, 370-411 A axes, Rayonix MX-300 marCCD, SBGrid 9), 7D98 (P6122, c 602 A, EIGER 4M miniCBF at 1.9 A, XRDa 13), 9V16 (P41212, c 451 A, EIGER1 16M HDF5, XRDa 338) and 4P8R (P6522, c 701 A, Rayonix MX-225 marCCD, IRRMC), tagged large-cell (plus long-axis / virus). References are the deposited space group, cell and resolution. 7D98 is pinned to its 250-frame miniCBF sweep: the HDF5 masters beside it repeat frames 61-260 in 60-frame pieces. 4P8R's archive ships per-frame .bz2 files, decompressed after extraction. EXTERNAL_TEST_DATA.md gains the five rows (DOIs resolved), the archive notes and the updated collection counts. Co-Authored-By: Claude Opus 5.5 (1M context) Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi --- docs/EXTERNAL_TEST_DATA.md | 32 ++++++++++++++++++++------------ tools/battery/open.json | 7 ++++++- 2 files changed, 26 insertions(+), 13 deletions(-) diff --git a/docs/EXTERNAL_TEST_DATA.md b/docs/EXTERNAL_TEST_DATA.md index 886640a26..770a08db5 100644 --- a/docs/EXTERNAL_TEST_DATA.md +++ b/docs/EXTERNAL_TEST_DATA.md @@ -39,6 +39,9 @@ the table below; the repositories themselves are cited in | [3MEB](https://www.rcsb.org/structure/3MEB) | IRRMC [10.18430/M33MEB](https://doi.org/10.18430/M33MEB) | Home source, Rigaku MicroMax-007 HF | 1.90 | P 1 21 1 | 58.6 101.2 81.5 90.0 90.6 90.0 | Rigaku Saturn 944 | Structure of cytoplasmic aspartate aminotransferase from giardia lamblia | | [3P85](https://www.rcsb.org/structure/3P85) | IRRMC [10.18430/M33P85](https://doi.org/10.18430/M33P85) | Home source, Rigaku FR-E+ SuperBright | 1.90 | P 63 2 2 | 127.3 127.3 72.9 90.0 90.0 120.0 | Rigaku Saturn 944+ | Crystal structure enoyl-coa hydratase from mycobacterium avium | | [3R6O](https://www.rcsb.org/structure/3R6O) | IRRMC [10.18430/M33R6O](https://doi.org/10.18430/M33R6O) | Home source, Rigaku FR-E+ SuperBright | 1.95 | I 41 | 90.7 90.7 76.1 90.0 90.0 90.0 | Rigaku Saturn 944+ | Crystal structure of a probable 2-hydroxyhepta-2,4-diene-1, 7-dioateisomerase from Mycobacterium abscessus | +| [4MTK](https://www.rcsb.org/structure/4MTK) | SBGrid [10.15785/sbgrid/235](https://doi.org/10.15785/sbgrid/235) | SLS X06SA | 3.32 | P 61 | 168.3 168.3 652.8 90.0 90.0 120.0 | PILATUS 6M | Crystal structure of PA0091 VgrG1, the central spike of the Type VI Secretion System | +| [4NWV](https://www.rcsb.org/structure/4NWV) | SBGrid [10.15785/sbgrid/9](https://doi.org/10.15785/sbgrid/9) | APS 21-ID-D | 3.25 | I 2 2 2 | 402.2 369.9 410.5 90.0 90.0 90.0 | Rayonix MX-300 | Crystal structure of Orsay virus-like particle | +| [4P8R](https://www.rcsb.org/structure/4P8R) | IRRMC [10.18430/m34p8r](https://doi.org/10.18430/m34p8r) | APS 21-ID-F | 2.20 | P 65 2 2 | 86.7 86.7 701.4 90.0 90.0 120.0 | Rayonix MX-225 | Structure of a glycosomal glyceraldehyde 3-phosphate dehydrogenase from Trypanosoma brucei | | [5CC8](https://www.rcsb.org/structure/5CC8) | IRRMC [10.18430/M35CC8](https://doi.org/10.18430/M35CC8) | Home source, Rigaku MicroMax-007 HF | 1.75 | P 21 21 2 | 87.1 93.8 72.5 90.0 90.0 90.0 | Rigaku Saturn 944+ | Structure of thiamine-monophosphate kinase from Acinetobacter baumannii in complex with AMPPNP | | [5EBI](https://www.rcsb.org/structure/5EBI) | MXRDR [10.18150/9887707](https://doi.org/10.18150/9887707) | BESSY 14.2 | 1.09 | P 1 21 1 | 35.7 44.1 35.7 90.0 120.0 90.0 | marCCD, 225 mm plate | Crystal structure of a DNA-RNA chimera in complex with Ba2+ ions: a case of unusual multi-domain twinning | | [5EPE](https://www.rcsb.org/structure/5EPE) | IRRMC [10.18430/m3159c](https://doi.org/10.18430/m3159c) | APS 21-ID-G | 1.90 | F 2 3 | 157.5 157.5 157.5 90.0 90.0 90.0 | Rayonix MX-300 | Crystal structure of SAM-dependent methyltransferase from Thiobacillus denitrificans in complex with S-Adenosyl-L-homocysteine | @@ -111,6 +114,7 @@ the table below; the repositories themselves are cited in | [7BGT](https://www.rcsb.org/structure/7BGT) | MXRDR [10.18150/1HQGWO](https://doi.org/10.18150/1HQGWO) | BESSY 14.2 | 1.93 | P 1 | 29.3 67.6 69.7 76.8 83.9 83.6 | marCCD, 225 mm plate | Mason-Pfizer Monkey Virus Protease mutant C7A/D26N/C106A in complex with peptidomimetic inhibitor | | [7BGU](https://www.rcsb.org/structure/7BGU) | MXRDR [10.18150/C9DYSH](https://doi.org/10.18150/C9DYSH) | EMBL/DESY Hamburg (DORIS) X13 | 2.43 | P 1 | 29.1 67.9 69.7 77.1 83.3 83.2 | marCCD 165 mm | Mason-Pfizer Monkey Virus Protease mutant C7A/D26N/C106A in complex with peptidomimetic inhibitor | | [7D1M](https://www.rcsb.org/structure/7D1M) | IRRMC [10.18430/m37brr](https://doi.org/10.18430/m37brr) | SSRF BL17U1 | 1.35 | P 1 21 1 | 55.5 99.0 59.6 90.0 108.5 90.0 | Dectris Eiger 16M | CRYSTAL STRUCTURE OF THE SARS-CoV-2 MAIN PROTEASE COMPLEXED WITH GC376 | +| [7D98](https://www.rcsb.org/structure/7D98) | XRDa [10.51093/xrd-00013](https://doi.org/10.51093/xrd-00013) | Photon Factory BL-1A | 3.60 | P 61 2 2 | 105.8 105.8 602.5 90.0 90.0 120.0 | Dectris Eiger 4M | Crystal structure of full-length CbnR complexed with the target DNA complex | | [7DKP](https://www.rcsb.org/structure/7DKP) | IRRMC [10.18430/M37DKP](https://doi.org/10.18430/M37DKP) | ESRF MASSIF-3 | 1.45 | P 1 21 1 | 49.8 169.5 49.8 90.0 93.5 90.0 | Dectris Eiger 4M | Crystal structure of E. coli Grx2 in complex with GSH at 1.45 A resolution | | [7K1L](https://www.rcsb.org/structure/7K1L) | IRRMC [10.18430/m37k1l](https://doi.org/10.18430/m37k1l) | APS 19-ID | 2.25 | P 63 | 150.8 150.8 110.7 90.0 90.0 120.0 | PILATUS3 6M | Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with Uridine-2',3'-Vanadate | | [7KCN](https://www.rcsb.org/structure/7KCN) | IRRMC [10.18430/m37kcn](https://doi.org/10.18430/m37kcn) | LNLS W01B-MX2 | 1.46 | P 41 2 2 | 67.0 67.0 116.9 90.0 90.0 90.0 | PILATUS 2M | Reconstructed ancestor of HIUases and Transthyretins | @@ -205,6 +209,7 @@ the table below; the repositories themselves are cited in | [9SL0](https://www.rcsb.org/structure/9SL0) | IRRMC [10.18430/M39SL0](https://doi.org/10.18430/M39SL0) | ESRF MASSIF-1 | 1.60 | P 21 21 21 | 60.2 80.2 111.6 90.0 90.0 90.0 | Dectris EIGER2 Si 9M | Crystal structure of HLA-A0201 in complex with peptide LLWNGPMAV | | [9T6S](https://www.rcsb.org/structure/9T6S) | SBGrid [10.15785/sbgrid/1260](https://doi.org/10.15785/sbgrid/1260) | ESRF ID30B | 2.00 | P 21 21 21 | 63.0 64.6 102.7 90.0 90.0 90.0 | Dectris EIGER2 Si 9M | Crystal Structure of the Listeria monocytogenes CadC with Cadmium | | [9UPT](https://www.rcsb.org/structure/9UPT) | XRDa [10.51093/xrd-00191](https://doi.org/10.51093/xrd-00191) | NSRRC TPS 05A | 2.37 | P 6 | 158.3 158.3 54.0 90.0 90.0 120.0 | SMV, S/N 930 | Structure of AtBgl1A, a GH1 beta-Glucosidase from Acetivibrio thermocellus | +| [9V16](https://www.rcsb.org/structure/9V16) | XRDa [10.51093/xrd-00338](https://doi.org/10.51093/xrd-00338) | SPring-8 BL44XU | 3.45 | P 41 21 2 | 185.6 185.6 451.2 90.0 90.0 90.0 | Dectris EIGER1 Si 16M | Crystal structure of E. coli glycogen phosphorylase N185A/R267E mutant in complex with AMP | | [9VX7](https://www.rcsb.org/structure/9VX7) | IRRMC [10.18430/M39VX7](https://doi.org/10.18430/M39VX7) | PAL/PLS 5C (4A) | 4.85 | P 64 | 122.5 122.5 118.9 90.0 90.0 120.0 | PILATUS3 6M | Transcription factor | | [9VYB](https://www.rcsb.org/structure/9VYB) | IRRMC [10.18430/M39VYB](https://doi.org/10.18430/M39VYB) | PAL/PLS 5C (4A) | 2.12 | P 21 21 21 | 44.4 47.8 48.4 90.0 90.0 90.0 | Dectris Eiger 9M | Antitoxin Phd | | [9W3Y](https://www.rcsb.org/structure/9W3Y) | IRRMC [10.18430/M39W3Y](https://doi.org/10.18430/M39W3Y) | Photon Factory BL-1A | 1.50 | P 21 21 21 | 60.7 70.0 94.2 90.0 90.0 90.0 | Dectris EIGER1 Si 4M | X-ray Crystal Structure of Pseudoazurin Met16Gly variant (Tris-HCl pH 7.6) | @@ -284,7 +289,7 @@ the rest were deleted, so a run over the data directory sees a single collection | 9CRW | a dose pair on one crystal 37 min apart - 0.025 s at 289 mm, 0.010 s at 276 mm | the 0.025 s sweep, whose 2.5 Å target matches the deposited 2.49 Å | | 7RIS | two crystals at two wavelengths - 1.53494 Å (Ho derivative) and 1.03329 Å (the deposited native) | **both** | -**Ten further archives hold more than one collection.** Their layout was read from the +**Eleven further archives hold more than one collection.** Their layout was read from the image files and repository listings; one sweep is kept for a run over the data directory unless noted. @@ -300,8 +305,9 @@ noted. | lalanine | four runs of the RODIN L-alanine deposition at 2θ = 20° | the 900-frame `pgw240050_01` run | | 9E2T | one continuous sweep plus screening images | the 2700-frame sweep | | 8OWM | three MXRDR zips covering one 1800-frame sweep, plus a processed-data zip | the three sweep zips (proc zip skipped) | +| 7D98 | one 250 × 0.5° miniCBF sweep (frames 11-260), plus four HDF5 masters that repeat frames 61-260 in 60-frame pieces | the miniCBF sweep; the HDF5 files stay beside it and the row is pinned | -**Two archives needed special handling to obtain the images.** +**Three archives needed special handling to obtain the images.** - **5KY6** is served by MXRDR as 11 separate RAR archives, one folder of frames per archive, 50 frames per archive except the last, 564 frames in all. Reading them needs a RAR reader with @@ -309,6 +315,8 @@ noted. of Enterprise Linux 8 cannot. - **6NEN**'s University of Queensland eSpace record blocks scripted download, so its archive was downloaded by hand in a browser. +- **4P8R**'s IRRMC tar holds one 800 × 0.2° sweep as per-frame `.bz2` files, which rugnux does + not read; they were decompressed with `bunzip2` after extraction. ## Datasets published as Raw Data Letters @@ -519,25 +527,25 @@ symmetries rather than to be easy to process. The counts below describe where it like everything else on this page, they are metadata about the depositions and their files, not measurements. -- **Repository:** IRRMC 94, SBGrid 36, Zenodo 34, MXRDR 16, Keele University 4, ESRF 3, XRDa 3, +- **Repository:** IRRMC 95, SBGrid 38, Zenodo 34, MXRDR 16, Keele University 4, ESRF 3, XRDa 5, UQ eSpace 1. - **Facility** - counted from the facility part of the Facility / beamline column, the beamline - ignored so that entries deposited with and without one count the same, over the 180 rows that - name one: APS 26, Diamond 20, ESRF 17, NSLS-II 14, BESSY 12, PETRA III 12, SSRL 11, ALS 8, - SLS 7, SOLEIL 7, SPring-8 7, SSRF 7, PAL/PLS 5, CHESS 4, CLSI 4, ALBA 3, Australian - Synchrotron 3, ELETTRA 2, LNLS 2, MAX IV 2, NSLS 2, and one each from NSRRC, Photon Factory, + ignored so that entries deposited with and without one count the same, over the 185 rows that + name one: APS 28, Diamond 20, ESRF 17, NSLS-II 14, BESSY 12, PETRA III 12, SSRL 11, ALS 8, + SLS 8, SPring-8 8, SOLEIL 7, SSRF 7, PAL/PLS 5, CHESS 4, CLSI 4, ALBA 3, Australian + Synchrotron 3, ELETTRA 2, LNLS 2, MAX IV 2, NSLS 2, Photon Factory 2, and one each from NSRRC, RRCAT Indus-2, SRS Daresbury and EMBL/DESY Hamburg (DORIS) - 26 facilities. The other ten rows were collected on laboratory sources: nine on rotating anodes and one on a liquid-metal jet. -- **Crystal system, from the deposited space group of the 184 PDB-coded rows:** orthorhombic 46, - monoclinic 44, tetragonal 30, trigonal 21, hexagonal 17, cubic 13, triclinic 13. -- **Pink beam:** none of these datasets was collected with pink beam. All 184 PDB-coded rows +- **Crystal system, from the deposited space group of the 189 PDB-coded rows:** orthorhombic 47, + monoclinic 44, tetragonal 31, trigonal 21, hexagonal 20, cubic 13, triclinic 13. +- **Pink beam:** none of these datasets was collected with pink beam. All 189 PDB-coded rows are deposited as `SINGLE WAVELENGTH` (`_diffrn_radiation.pdbx_diffrn_protocol`), and all but 5REO, which leaves the field blank, as monochromatic (`pdbx_monochromatic_or_laue_m_l` `M`); 9Q41 is the one row recorded with a multilayer rather than a crystal monochromator (CHESS Rh/B4C). The battery's pink-beam data are in-house SLS measurements (tag `pink-beam` in `tools/battery/inhouse.json`), not on this page. -- **Long cell axes:** eleven PDB-coded rows have a deposited cell axis longer than 320 Å - 8V4O, - 9ZMU, 9Z72, 9YL4, 5NW5, 6QAJ, 7QIJ, 8T7R, 9H0Q, 6G1F and 6OEL. +- **Long cell axes:** sixteen PDB-coded rows have a deposited cell axis longer than 320 Å - 4P8R, + 4MTK, 7D98, 8V4O, 9ZMU, 9V16, 9Z72, 4NWV, 9YL4, 5NW5, 6QAJ, 7QIJ, 8T7R, 9H0Q, 6G1F and 6OEL. The marCCD, SMV and gzip-compressed miniCBF datasets are the reason rugnux reads those formats natively, and accepts the `.img` and numeric-suffix (`.001`) file names they arrive with. diff --git a/tools/battery/open.json b/tools/battery/open.json index 1ee69a458..e5b8f49c8 100644 --- a/tools/battery/open.json +++ b/tools/battery/open.json @@ -201,5 +201,10 @@ {"id": "6cs9", "input": "6cs9/568/HBD2D7_2_1_001.img", "wavelength": 0.9537, "ref": {"sg": "P 1 21 1", "sgno": 4, "cell": [32.871, 25.538, 40.17, 90.0, 98.64, 90.0], "dmin": 1.85}, "tags": ["smv", "monoclinic"]}, {"id": "9lxl", "input": "9lxl/6/1_T10Y-FFp-PNPI_6_master.h5", "wavelength": 0.97919, "ref": {"sg": "P 41 21 2", "sgno": 92, "cell": [76.757, 76.757, 225.338, 90.0, 90.0, 90.0], "dmin": 2.191}, "tags": ["h5", "tetragonal"]}, {"id": "9s02", "input": "9s02/PYCR1-D11_1_master.h5", "wavelength": 0.97625, "ref": {"sg": "P 21 21 2", "sgno": 18, "cell": [163.674, 88.042, 116.731, 90.0, 90.0, 90.0], "dmin": 1.65}, "tags": ["h5", "orthorhombic"], "tiers": {"ci": "HDF5, orthorhombic P21212"}}, - {"id": "6gvk", "input": "6gvk/212_3_0001.cbf", "wavelength": 0.97915, "ref": {"sg": "C 1 2 1", "sgno": 5, "cell": [105.58, 59.52, 42.4, 90.0, 113.5, 90.0], "dmin": 1.55}, "tags": ["cbf", "monoclinic"], "pinned": true, "tiers": {"ci": "C-centred monoclinic C2"}} + {"id": "6gvk", "input": "6gvk/212_3_0001.cbf", "wavelength": 0.97915, "ref": {"sg": "C 1 2 1", "sgno": 5, "cell": [105.58, 59.52, 42.4, 90.0, 113.5, 90.0], "dmin": 1.55}, "tags": ["cbf", "monoclinic"], "pinned": true, "tiers": {"ci": "C-centred monoclinic C2"}}, + {"id": "4mtk", "input": "4mtk/sbgrid235/lambda_1.0A_1_00001.cbf", "wavelength": 1.0, "ref": {"sg": "P 61", "sgno": 169, "cell": [168.275, 168.275, 652.849, 90.0, 90.0, 120.0], "dmin": 3.322}, "tags": ["cbf", "hexagonal", "large-cell", "long-axis"]}, + {"id": "4nwv", "input": "4nwv/sbgrid9/formal.001", "wavelength": 1.12706, "ref": {"sg": "I 2 2 2", "sgno": 23, "cell": [402.197, 369.862, 410.511, 90.0, 90.0, 90.0], "dmin": 3.25}, "tags": ["marCCD", "orthorhombic", "large-cell", "virus"]}, + {"id": "7d98", "input": "7d98/xrda13/data/cbnrf006_01_00011.cbf", "wavelength": 1.9, "ref": {"sg": "P 61 2 2", "sgno": 178, "cell": [105.819, 105.819, 602.516, 90.0, 90.0, 120.0], "dmin": 3.6}, "tags": ["cbf", "hexagonal", "large-cell", "long-axis", "long-wavelength"], "pinned": true}, + {"id": "9v16", "input": "9v16/xrd-00338/9V16/data01_master.h5", "wavelength": 0.9, "ref": {"sg": "P 41 21 2", "sgno": 92, "cell": [185.604, 185.604, 451.242, 90.0, 90.0, 90.0], "dmin": 3.45}, "tags": ["h5", "tetragonal", "large-cell", "long-axis"]}, + {"id": "4p8r", "input": "4p8r/data/4p8r/series/gzn0-7.001", "wavelength": 0.97872, "ref": {"sg": "P 65 2 2", "sgno": 179, "cell": [86.7, 86.7, 701.37, 90.0, 90.0, 120.0], "dmin": 2.2}, "tags": ["marCCD", "hexagonal", "large-cell", "long-axis"]} ]}