Merge branch 'battery-large-cells' into rc175: five large-cell open-arm sets (4mtk, 4nwv, 7d98, 9v16, 4p8r)
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi
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Claude Opus 5.5
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@@ -39,6 +39,9 @@ the table below; the repositories themselves are cited in
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| [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 |
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| [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 |
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| [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 |
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| [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 |
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| [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 |
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| [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 |
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| [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 |
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| [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 |
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| [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 |
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@@ -111,6 +114,7 @@ the table below; the repositories themselves are cited in
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| [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 |
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| [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 |
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| [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 |
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| [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 |
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| [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 |
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| [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 |
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| [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 |
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@@ -205,6 +209,7 @@ the table below; the repositories themselves are cited in
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| [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 |
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| [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 |
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| [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 |
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| [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 |
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| [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 |
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| [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 |
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| [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) |
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@@ -284,7 +289,7 @@ the rest were deleted, so a run over the data directory sees a single collection
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| 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 |
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| 7RIS | two crystals at two wavelengths - 1.53494 Å (Ho derivative) and 1.03329 Å (the deposited native) | **both** |
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**Ten further archives hold more than one collection.** Their layout was read from the
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**Eleven further archives hold more than one collection.** Their layout was read from the
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image files and repository listings; one sweep is kept for a run over the data directory unless
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noted.
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@@ -300,8 +305,9 @@ noted.
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| lalanine | four runs of the RODIN L-alanine deposition at 2θ = 20° | the 900-frame `pgw240050_01` run |
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| 9E2T | one continuous sweep plus screening images | the 2700-frame sweep |
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| 8OWM | three MXRDR zips covering one 1800-frame sweep, plus a processed-data zip | the three sweep zips (proc zip skipped) |
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| 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 |
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**Two archives needed special handling to obtain the images.**
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**Three archives needed special handling to obtain the images.**
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- **5KY6** is served by MXRDR as 11 separate RAR archives, one folder of frames per archive, 50
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frames per archive except the last, 564 frames in all. Reading them needs a RAR reader with
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@@ -309,6 +315,8 @@ noted.
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of Enterprise Linux 8 cannot.
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- **6NEN**'s University of Queensland eSpace record blocks scripted download, so its archive was
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downloaded by hand in a browser.
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- **4P8R**'s IRRMC tar holds one 800 × 0.2° sweep as per-frame `.bz2` files, which rugnux does
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not read; they were decompressed with `bunzip2` after extraction.
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## Datasets published as Raw Data Letters
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@@ -519,25 +527,25 @@ symmetries rather than to be easy to process. The counts below describe where it
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like everything else on this page, they are metadata about the depositions and their files, not
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measurements.
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- **Repository:** IRRMC 94, SBGrid 36, Zenodo 34, MXRDR 16, Keele University 4, ESRF 3, XRDa 3,
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- **Repository:** IRRMC 95, SBGrid 38, Zenodo 34, MXRDR 16, Keele University 4, ESRF 3, XRDa 5,
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UQ eSpace 1.
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- **Facility** - counted from the facility part of the Facility / beamline column, the beamline
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ignored so that entries deposited with and without one count the same, over the 180 rows that
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name one: APS 26, Diamond 20, ESRF 17, NSLS-II 14, BESSY 12, PETRA III 12, SSRL 11, ALS 8,
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SLS 7, SOLEIL 7, SPring-8 7, SSRF 7, PAL/PLS 5, CHESS 4, CLSI 4, ALBA 3, Australian
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Synchrotron 3, ELETTRA 2, LNLS 2, MAX IV 2, NSLS 2, and one each from NSRRC, Photon Factory,
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ignored so that entries deposited with and without one count the same, over the 185 rows that
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name one: APS 28, Diamond 20, ESRF 17, NSLS-II 14, BESSY 12, PETRA III 12, SSRL 11, ALS 8,
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SLS 8, SPring-8 8, SOLEIL 7, SSRF 7, PAL/PLS 5, CHESS 4, CLSI 4, ALBA 3, Australian
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Synchrotron 3, ELETTRA 2, LNLS 2, MAX IV 2, NSLS 2, Photon Factory 2, and one each from NSRRC,
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RRCAT Indus-2, SRS Daresbury and EMBL/DESY Hamburg (DORIS) - 26 facilities. The other ten rows were collected on laboratory sources: nine on
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rotating anodes and one on a liquid-metal jet.
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- **Crystal system, from the deposited space group of the 184 PDB-coded rows:** orthorhombic 46,
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monoclinic 44, tetragonal 30, trigonal 21, hexagonal 17, cubic 13, triclinic 13.
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- **Pink beam:** none of these datasets was collected with pink beam. All 184 PDB-coded rows
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- **Crystal system, from the deposited space group of the 189 PDB-coded rows:** orthorhombic 47,
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monoclinic 44, tetragonal 31, trigonal 21, hexagonal 20, cubic 13, triclinic 13.
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- **Pink beam:** none of these datasets was collected with pink beam. All 189 PDB-coded rows
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are deposited as `SINGLE WAVELENGTH` (`_diffrn_radiation.pdbx_diffrn_protocol`), and all
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but 5REO, which leaves the field blank, as monochromatic (`pdbx_monochromatic_or_laue_m_l`
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`M`); 9Q41 is the one row recorded with a multilayer rather than a crystal monochromator
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(CHESS Rh/B4C). The battery's pink-beam data are in-house SLS measurements (tag `pink-beam`
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in `tools/battery/inhouse.json`), not on this page.
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- **Long cell axes:** eleven PDB-coded rows have a deposited cell axis longer than 320 Å - 8V4O,
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9ZMU, 9Z72, 9YL4, 5NW5, 6QAJ, 7QIJ, 8T7R, 9H0Q, 6G1F and 6OEL.
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- **Long cell axes:** sixteen PDB-coded rows have a deposited cell axis longer than 320 Å - 4P8R,
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4MTK, 7D98, 8V4O, 9ZMU, 9V16, 9Z72, 4NWV, 9YL4, 5NW5, 6QAJ, 7QIJ, 8T7R, 9H0Q, 6G1F and 6OEL.
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The marCCD, SMV and gzip-compressed miniCBF datasets are the reason rugnux reads those formats
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natively, and accepts the `.img` and numeric-suffix (`.001`) file names they arrive with.
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@@ -201,5 +201,10 @@
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{"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"]},
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{"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"]},
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{"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"}},
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{"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"}}
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{"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"}},
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{"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"]},
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{"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"]},
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{"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},
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{"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"]},
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{"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"]}
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]}
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