pdb_id large_stringlengths 4 4 | crystal_id large_stringclasses 26
values | component_index uint16 0 34 ⌀ | role large_stringclasses 9
values | name_raw large_stringlengths 2 200 ⌀ | name_canonical large_stringclasses 487
values | chem_class large_stringclasses 9
values | peg_mw int32 200 35k ⌀ | is_mme bool 2
classes | hofmeister_rank int32 -4 4 ⌀ | buffer_pka float64 1.92 10.4 ⌀ | concentration float64 0 1.21M ⌀ | unit large_stringclasses 8
values | unit_inferred bool 2
classes | concentration_is_range bool 2
classes | range_low float64 0 2.02k ⌀ | range_high float64 0 1.51k ⌀ | cryo_evidence large_stringclasses 2
values | premix_id large_stringclasses 24
values | parser large_stringclasses 3
values |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
10HT | 1 | 0 | buffer | mops | MOPS | buffer | null | false | null | 7.2 | 100 | millimolar | false | false | null | null | null | null | rules |
10HT | 1 | 1 | salt | magnesium sulfate | MAGNESIUM_SULFATE | salt | null | false | -4 | null | 1.25 | molar | false | false | null | null | null | null | rules |
10IA | 1 | 0 | precipitant | peg 8000 | PEG_8000 | peg | 8,000 | false | null | null | 11 | percent_w_v | true | false | null | null | null | null | rules |
10IA | 1 | 1 | precipitant | ethylene glycol | ETHYLENE_GLYCOL | polyol | null | false | null | null | 17.5 | percent_v_v | true | true | 15 | 20 | null | null | rules |
10IA | 1 | 2 | buffer | mes | MES | buffer | null | false | null | 6.15 | 0.1 | molar | false | false | null | null | null | null | rules |
10IA | 1 | 3 | additive | 6-aminohexanoic acid | AMINOHEXANOIC_ACID_6 | additive | null | false | null | null | 5 | percent_w_v | true | false | null | null | null | null | rules |
10KY | 1 | 0 | salt | ammonium sulfate | AMMONIUM_SULFATE | salt | null | false | -4 | null | 0.2 | molar | false | false | null | null | null | null | rules |
10KY | 1 | 1 | salt | sodium chloride | SODIUM_CHLORIDE | salt | null | false | 0 | null | 0.02 | molar | false | false | null | null | null | null | rules |
10KY | 1 | 2 | buffer | sodium acetate | SODIUM_ACETATE | buffer | null | false | -2 | 4.76 | 0.02 | molar | false | false | null | null | null | null | rules |
10KY | 1 | 3 | precipitant | peg 200 | PEG_200 | peg | 200 | false | null | null | 33 | percent_v_v | true | false | null | null | null | null | rules |
10NV | 1 | 0 | precipitant | peg 4000 | PEG_4000 | peg | 4,000 | false | null | null | 27 | percent_w_v | true | true | 25 | 29 | null | null | rules |
10NV | 1 | 1 | salt | cacl2 | CALCIUM_CHLORIDE | salt | null | false | 0 | null | 0.2 | molar | false | false | null | null | null | null | rules |
10NV | 1 | 2 | buffer | tris | TRIS | buffer | null | false | null | 8.06 | 0.1 | molar | false | false | null | null | null | null | rules |
10PA | 1 | 0 | salt | calcium chloride | CALCIUM_CHLORIDE | salt | null | false | 0 | null | 0.2 | molar | false | false | null | null | null | null | rules |
10PA | 1 | 1 | precipitant | peg 3350 | PEG_3350 | peg | 3,350 | false | null | null | 20 | percent_w_v | false | false | null | null | null | null | rules |
10PI | 1 | 0 | buffer | bis-tris-propane | BIS_TRIS_PROPANE | buffer | null | false | null | 6.8 | 0.1 | molar | false | false | null | null | null | null | rules |
10PI | 1 | 1 | precipitant | peg 3350 | PEG_3350 | peg | 3,350 | false | null | null | 20 | percent_w_v | false | false | null | null | null | null | rules |
10PI | 1 | 2 | unknown | k2-h-phosphate | null | null | null | false | null | null | 5 | millimolar | false | false | null | null | null | null | rules |
10PI | 1 | 3 | unknown | k-h2-phosphate | null | null | null | false | null | null | 5 | millimolar | false | false | null | null | null | null | rules |
10PI | 1 | 4 | unknown | na2-h-phosphate | null | null | null | false | null | null | 5 | millimolar | false | false | null | null | null | null | rules |
10PI | 1 | 5 | unknown | na-h2-phosphate | null | null | null | false | null | null | 5 | millimolar | false | false | null | null | null | null | rules |
10QI | 1 | 0 | buffer | bis-tris | BIS_TRIS | buffer | null | false | null | 6.5 | 100 | millimolar | false | false | null | null | null | null | rules |
10QI | 1 | 1 | unknown | cadmium chliride | null | null | null | false | null | null | 20 | millimolar | false | false | null | null | null | null | rules |
10QI | 1 | 2 | precipitant | peg 400 | PEG_400 | peg | 400 | false | null | null | 23 | percent_v_v | true | false | null | null | null | null | rules |
10QI | 1 | 3 | unknown | 3'-sialyllactose | null | null | null | false | null | null | 5 | millimolar | false | false | null | null | null | null | rules |
10QS | 1 | 0 | buffer | mes | MES | buffer | null | false | null | 6.15 | 0.1 | molar | false | false | null | null | null | null | rules |
10QS | 1 | 1 | precipitant | peg 8000 | PEG_8000 | peg | 8,000 | false | null | null | 24 | percent_w_v | true | false | null | null | null | null | rules |
10QS | 1 | 2 | cryo | glycerol | GLYCEROL | polyol | null | false | null | null | 5 | percent_v_v | true | false | null | null | inferred | null | rules |
10RA | 1 | 0 | buffer | bis-tris propane | BIS_TRIS_PROPANE | buffer | null | false | null | 6.8 | 0.1 | molar | false | false | null | null | null | null | rules |
10RA | 1 | 1 | salt | potassium thiocyanate | POTASSIUM_THIOCYANATE | salt | null | false | 4 | null | 0.2 | molar | false | false | null | null | null | null | rules |
10RA | 1 | 2 | precipitant | peg 3350 | PEG_3350 | peg | 3,350 | false | null | null | 12 | percent_w_v | false | false | null | null | null | null | rules |
10XD | 1 | 0 | salt | ammonium citrate tribasic | AMMONIUM_CITRATE | salt | null | false | -3 | null | 1.3 | molar | false | false | null | null | null | null | rules |
10XD | 1 | 1 | buffer | bis-tris propane | BIS_TRIS_PROPANE | buffer | null | false | null | 6.8 | 0.1 | molar | false | false | null | null | null | null | rules |
10YZ | 1 | 0 | precipitant | peg 3350 | PEG_3350 | peg | 3,350 | false | null | null | 20 | percent_w_v | false | false | null | null | null | null | rules |
110M | 1 | 0 | salt | ammonium sulfate | AMMONIUM_SULFATE | salt | null | false | -4 | null | 3 | molar | false | false | null | null | null | null | rules |
110M | 1 | 1 | buffer | tris | TRIS | buffer | null | false | null | 8.06 | 20 | millimolar | false | false | null | null | null | null | rules |
110M | 1 | 2 | additive | edta | EDTA | additive | null | false | null | null | 1 | millimolar | false | false | null | null | null | null | rules |
11FC | 1 | 0 | salt | ammonium citrate dibasic | AMMONIUM_CITRATE | salt | null | false | -3 | null | 0.2 | molar | false | false | null | null | null | null | rules |
11FC | 1 | 1 | precipitant | peg 3350 | PEG_3350 | peg | 3,350 | false | null | null | 20 | percent_w_v | false | false | null | null | null | null | rules |
11GX | 1 | 0 | buffer | sodium citrate | SODIUM_CITRATE | buffer | null | false | -3 | 4.76 | 0.1 | molar | false | false | null | null | null | null | rules |
11GX | 1 | 1 | precipitant | peg 4000 | PEG_4000 | peg | 4,000 | false | null | null | 20 | percent_w_v | false | false | null | null | null | null | rules |
11GX | 1 | 2 | precipitant | 2-propanol | ISOPROPANOL | organic | null | false | null | null | 20 | percent_v_v | false | false | null | null | null | null | rules |
11MQ | 1 | 0 | salt | lithium sulfate | LITHIUM_SULFATE | salt | null | false | -4 | null | 0.2 | molar | false | false | null | null | null | null | rules |
11MQ | 1 | 1 | salt | zinc acetate | ZINC_ACETATE | salt | null | false | -2 | null | 0.5 | molar | false | false | null | null | null | null | rules |
11MQ | 1 | 2 | buffer | bistris | BIS_TRIS | buffer | null | false | null | 6.5 | 0.1 | molar | false | false | null | null | null | null | rules |
11MQ | 1 | 3 | precipitant | peg smear broad | PEG_SMEAR_BROAD | other | null | false | null | null | 22.5 | percent_v_v | false | false | null | null | null | null | rules |
11MQ | 1 | 4 | unknown | peg smear broad contains | null | null | null | false | null | null | null | null | false | false | null | null | null | null | rules |
11MQ | 1 | 5 | precipitant | peg 1000 | PEG_1000 | peg | 1,000 | false | null | null | null | percent_w_v | true | false | null | null | null | null | rules |
11MQ | 1 | 6 | precipitant | peg 10000 | PEG_10000 | peg | 10,000 | false | null | null | null | percent_w_v | true | false | null | null | null | null | rules |
11MQ | 1 | 7 | precipitant | peg 2000 | PEG_2000 | peg | 2,000 | false | null | null | null | percent_w_v | true | false | null | null | null | null | rules |
11MQ | 1 | 8 | precipitant | peg 3350 | PEG_3350 | peg | 3,350 | false | null | null | null | percent_w_v | true | false | null | null | null | null | rules |
11MQ | 1 | 9 | precipitant | peg 400 | PEG_400 | peg | 400 | false | null | null | null | percent_v_v | true | false | null | null | null | null | rules |
11MQ | 1 | 10 | precipitant | peg 4000 | PEG_4000 | peg | 4,000 | false | null | null | null | percent_w_v | true | false | null | null | null | null | rules |
11MQ | 1 | 11 | precipitant | peg 600 | PEG_600 | peg | 600 | false | null | null | null | percent_v_v | true | false | null | null | null | null | rules |
11MQ | 1 | 12 | precipitant | peg 6000 | PEG_6000 | peg | 6,000 | false | null | null | null | percent_w_v | true | false | null | null | null | null | rules |
11MQ | 1 | 13 | precipitant | peg 8000 | PEG_8000 | peg | 8,000 | false | null | null | null | percent_w_v | true | false | null | null | null | null | rules |
11MQ | 1 | 14 | unknown | peg methyl ether 500 | null | null | null | false | null | null | null | null | false | false | null | null | null | null | rules |
11MQ | 1 | 15 | unknown | peg methyl ether 5000 | null | null | null | false | null | null | null | null | false | false | null | null | null | null | rules |
11ZT | 1 | 0 | salt | sodium thiocyanate | SODIUM_THIOCYANATE | salt | null | false | 4 | null | 0.1 | molar | false | false | null | null | null | null | rules |
11ZT | 1 | 1 | precipitant | peg 3350 | PEG_3350 | peg | 3,350 | false | null | null | 10 | percent_w_v | true | false | null | null | null | null | rules |
12UQ | 1 | 0 | precipitant | peg mme 2000 | PEG_MME_2000 | peg | 2,000 | true | null | null | 26 | percent_w_v | false | false | null | null | null | null | rules |
12UQ | 1 | 1 | buffer | bis-tris | BIS_TRIS | buffer | null | false | null | 6.5 | 0.1 | molar | false | false | null | null | null | null | rules |
13MX | 1 | 0 | buffer | sodium maleate | SODIUM_MALEATE | buffer | null | false | null | 6.2 | 1.4 | molar | false | false | null | null | null | null | rules |
13NM | 1 | 0 | buffer | sodium maleate | SODIUM_MALEATE | buffer | null | false | null | 6.2 | 1.4 | molar | false | false | null | null | null | null | rules |
13NR | 1 | 0 | buffer | sodium maleate | SODIUM_MALEATE | buffer | null | false | null | 6.2 | 1.4 | molar | false | false | null | null | null | null | rules |
13OH | 1 | 0 | buffer | sodium maleate | SODIUM_MALEATE | buffer | null | false | null | 6.2 | 1.4 | molar | false | false | null | null | null | null | rules |
13ON | 1 | 0 | buffer | sodium maleate | SODIUM_MALEATE | buffer | null | false | null | 6.2 | 1.4 | molar | false | false | null | null | null | null | rules |
13PI | 1 | 0 | buffer | sodium maleate | SODIUM_MALEATE | buffer | null | false | null | 6.2 | 1.4 | molar | false | false | null | null | null | null | rules |
13QQ | 1 | 0 | buffer | sodium maleate | SODIUM_MALEATE | buffer | null | false | null | 6.2 | 1.4 | molar | false | false | null | null | null | null | rules |
13RC | 1 | 0 | buffer | sodium maleate | SODIUM_MALEATE | buffer | null | false | null | 6.2 | 1.4 | molar | false | false | null | null | null | null | rules |
13RK | 1 | 0 | buffer | ches | CHES | buffer | null | false | null | 9.3 | 100 | millimolar | false | false | null | null | null | null | rules |
13RK | 1 | 1 | precipitant | peg 3000 | PEG_3000 | peg | 3,000 | false | null | null | 28 | percent_w_v | true | false | null | null | null | null | rules |
13RT | 1 | 0 | buffer | ches | CHES | buffer | null | false | null | 9.3 | 100 | millimolar | false | false | null | null | null | null | rules |
13RT | 1 | 1 | precipitant | peg 3000 | PEG_3000 | peg | 3,000 | false | null | null | 28 | percent_w_v | true | false | null | null | null | null | rules |
13RX | 1 | 0 | buffer | ches | CHES | buffer | null | false | null | 9.3 | 100 | millimolar | false | false | null | null | null | null | rules |
13RX | 1 | 1 | precipitant | peg 3000 | PEG_3000 | peg | 3,000 | false | null | null | 28 | percent_w_v | true | false | null | null | null | null | rules |
13SK | 1 | 0 | buffer | sodium acetate | SODIUM_ACETATE | buffer | null | false | -2 | 4.76 | 200 | millimolar | false | false | null | null | null | null | rules |
13SK | 1 | 1 | buffer | tris | TRIS | buffer | null | false | null | 8.06 | 100 | millimolar | false | false | null | null | null | null | rules |
13SK | 1 | 2 | precipitant | peg 4000 | PEG_4000 | peg | 4,000 | false | null | null | 30 | percent_w_v | false | false | null | null | null | null | rules |
13YH | 1 | 0 | buffer | tris-hcl | TRIS | buffer | null | false | null | 8.06 | 0.1 | molar | false | false | null | null | null | null | rules |
13YH | 1 | 1 | precipitant | peg 3350 | PEG_3350 | peg | 3,350 | false | null | null | 16 | percent_w_v | true | false | null | null | null | null | rules |
13YH | 1 | 2 | precipitant | isopropanol | ISOPROPANOL | organic | null | false | null | null | 16 | percent_v_v | true | false | null | null | null | null | rules |
13ZC | 1 | 0 | buffer | tris-hcl | TRIS | buffer | null | false | null | 8.06 | 0.1 | molar | false | false | null | null | null | null | rules |
13ZC | 1 | 1 | precipitant | peg 3350 | PEG_3350 | peg | 3,350 | false | null | null | 16 | percent_w_v | true | false | null | null | null | null | rules |
13ZC | 1 | 2 | precipitant | isopropanol | ISOPROPANOL | organic | null | false | null | null | 16 | percent_v_v | true | false | null | null | null | null | rules |
13ZV | 1 | 0 | buffer | tris-hcl | TRIS | buffer | null | false | null | 8.06 | 0.1 | molar | false | false | null | null | null | null | rules |
13ZV | 1 | 1 | precipitant | peg 3350 | PEG_3350 | peg | 3,350 | false | null | null | 16 | percent_w_v | true | false | null | null | null | null | rules |
13ZV | 1 | 2 | precipitant | isopropanol | ISOPROPANOL | organic | null | false | null | null | 16 | percent_v_v | true | false | null | null | null | null | rules |
13ZZ | 1 | 0 | buffer | tris-hcl | TRIS | buffer | null | false | null | 8.06 | 0.1 | molar | false | false | null | null | null | null | rules |
13ZZ | 1 | 1 | precipitant | peg 3350 | PEG_3350 | peg | 3,350 | false | null | null | 16 | percent_w_v | true | false | null | null | null | null | rules |
13ZZ | 1 | 2 | precipitant | isopropanol | ISOPROPANOL | organic | null | false | null | null | 16 | percent_v_v | true | false | null | null | null | null | rules |
1A0U | 1 | 0 | precipitant | peg 6000 | PEG_6000 | peg | 6,000 | false | null | null | 10.5 | percent_w_v | true | false | null | null | null | null | rules |
1A0U | 1 | 1 | buffer | potassium phosphate | POTASSIUM_PHOSPHATE | buffer | null | false | -3 | 7.2 | 10 | millimolar | false | false | null | null | null | null | rules |
1A0U | 1 | 2 | salt | potassium chloride | POTASSIUM_CHLORIDE | salt | null | false | 0 | null | 100 | millimolar | false | false | null | null | null | null | rules |
1A0U | 1 | 3 | additive | sodium dithionite | SODIUM_DITHIONITE | additive | null | false | null | null | 3 | millimolar | false | false | null | null | null | null | rules |
1A2J | 1 | 0 | precipitant | peg 4k | PEG_4000 | peg | 4,000 | false | null | null | 27 | percent_w_v | true | false | null | null | null | null | rules |
1A2J | 1 | 1 | buffer | acetate | SODIUM_ACETATE | buffer | null | false | -2 | 4.76 | 0.1 | molar | false | false | null | null | null | null | rules |
1A34 | 1 | 0 | unknown | protein was four times recrystallized from bulk solution by addition af ammonium sulfate to 15% saturation | null | null | null | false | null | null | null | null | false | false | null | null | null | null | rules |
1A3Q | 1 | 0 | salt | mgso4 | MAGNESIUM_SULFATE | salt | null | false | -4 | null | 5 | millimolar | false | false | null | null | null | null | rules |
1A3Q | 1 | 1 | buffer | mes | MES | buffer | null | false | null | 6.15 | 50 | millimolar | false | false | null | null | null | null | rules |
End of preview. Expand in Data Studio
TopPDBLX v1.0.0
Every crystallisation condition in the Protein Data Bank, parsed, normalised and linked to the sequence that produced it.
Citable archive: 10.5281/zenodo.21807134 · Code: bellcheddar/TopPDBLX
The PDB holds about 200,000 crystallisation recipes, each typed free-hand in no agreed format. This dataset turns the free-text _exptl_crystal_grow.pdbx_details field into typed components (reagent, concentration, unit, role), cross-references them against published commercial screen formulations, and attaches MMseqs2 cluster identifiers so redundancy can be controlled.
| Records | 199,185 from 198,691 PDB entries, keyed on (pdb_id, crystal_id) |
| Components | 645,656, of which 87.3% resolve to a canonical reagent |
| Reagent lexicon | 500 curated reagents, 1,587 spellings |
| Sequence linkage | 195,985 records with UniProt accessions and clusters at 30/50/90% identity |
| Screen matches | 81,802 records matched to a well in one of 9 commercial screens |
| Classification | 152,006 conditions in a seven-class precipitant ontology |
Provenance: every component says which parser produced it
parser |
rows | what it is |
|---|---|---|
rules |
610,076 | A deterministic rule parser. Filter to this for a fully reproducible subset with no model output |
slm |
35,580 | Chemistry the rules left unnamed, recovered by a LoRA fine-tune of SmolLM2-360M reading the residual |
Against 192 hand-labelled records the combination reaches 93.3% precision and 90.3% recall for reagent identity, against the rule parser alone at 95.1% and 69.5%.
Read this first
The PDB contains only successes. Every condition here produced a crystal, so this supports P(condition | crystallised) and says nothing about P(crystallised | sequence). Condition frequency reflects screen popularity, not intrinsic success rate, and reported conditions are often optimised rather than screen hits. DATASHEET.md carries the full set of limitations, and reading it before drawing conclusions is not optional.
Files
| File | Contents |
|---|---|
toppdblx-conditions-v1.0.0.parquet |
Record level, sequence linkage flattened on |
toppdblx-components-v1.0.0.parquet |
One row per reagent |
toppdblx-components-v1.0.0.csv.gz |
The same, for spreadsheets |
schema-v1.0.0.json |
JSON Schema, generated from the pydantic model |
DATASHEET.md |
Datasheet, generated from the data at release time |
Data is CC-BY-4.0. Attribution does not discharge the obligation to the sources this derives from: the Protein Data Bank (CC0), SIFTS and UniProt.
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