Phase 6C.1 · Original deposited experimental coordinates

Comprehensive structure quality

Residue and heavy-atom completeness calculated directly from 230 source PDBx/mmCIF files, each verified against its frozen historical checksum. Each mapped PWWP chain/domain, NMR model and qualified source-supported ligand environment is tracked individually.

230Historically verified coordinate files

496Chain/domains with an observed PWWP core

283Source-supported ligand environments calculated

170Mapped chain/domains lacking observed core coordinates

Experimental-coordinate case studies

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9FOC · NSD2 PWWP1

Newly assessed ligand-bearing structure

Protein and bound ligand coordinates are deposited, but the literature's assayed compound 11 preparation remains stereochemically unresolved. Structural components do not fix that ambiguity.

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2M16 · PSIP1 PWWP

Deposited NMR ensemble

All model-specific atom observations are retained. Ensemble variation is not represented by a single first-model structure alone.

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11OA · DNMT3A PWWP1

Independently confirmed side-chain gaps

Five observed-core chains each lack 198 standard side-chain heavy atoms; 13 other mapped chains contain no observed core coordinates.

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All 666 original chain/domain mappings

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51 matching chain/domain records. Filters must be satisfied by the same experimental chain/domain. Model-specific assessment is available within each detail record.

PDB · chain	Target/domain	Core observed	Experiment	Missing side-chain atoms	Backbone gaps	Research ligand environments	Assessment
29HG · B	NSD2 PWWP1	65 / 65	ELECTRON MICROSCOPY · 4.0 Å	19	0	1	atomic completeness calculated
29HH · B	NSD2 PWWP1	65 / 65	ELECTRON MICROSCOPY · 4.2 Å	19	0	1	atomic completeness calculated
29HI · B	NSD2 PWWP1	65 / 65	ELECTRON MICROSCOPY · 5.9 Å	19	0	1	atomic completeness calculated
5VC8 · A	NSD2 PWWP1	60 / 65	X-RAY DIFFRACTION · 1.8 Å	10	0	0	atomic completeness calculated with chemistry limitations
5VC8 · B	NSD2 PWWP1	65 / 65	X-RAY DIFFRACTION · 1.8 Å	17	0	0	atomic completeness calculated with chemistry limitations
6UE6 · A	NSD2 PWWP1	62 / 65	X-RAY DIFFRACTION · 2.4 Å	19	0	2	atomic completeness calculated
6UE6 · B	NSD2 PWWP1	65 / 65	X-RAY DIFFRACTION · 2.4 Å	25	0	2	atomic completeness calculated
6UE6 · C	NSD2 PWWP1	62 / 65	X-RAY DIFFRACTION · 2.4 Å	12	2	2	atomic completeness calculated
6UE6 · D	NSD2 PWWP1	61 / 65	X-RAY DIFFRACTION · 2.4 Å	19	3	2	atomic completeness calculated
6UE6 · E	NSD2 PWWP1	63 / 65	X-RAY DIFFRACTION · 2.4 Å	29	2	2	atomic completeness calculated
6UE6 · F	NSD2 PWWP1	60 / 65	X-RAY DIFFRACTION · 2.4 Å	14	0	2	atomic completeness calculated
6UE6 · G	NSD2 PWWP1	62 / 65	X-RAY DIFFRACTION · 2.4 Å	12	0	2	atomic completeness calculated
6UE6 · H	NSD2 PWWP1	60 / 65	X-RAY DIFFRACTION · 2.4 Å	10	0	2	atomic completeness calculated
6XCG · A	NSD2 PWWP1	65 / 65	X-RAY DIFFRACTION · 1.64 Å	6	0	1	atomic completeness calculated
6XCG · B	NSD2 PWWP1	65 / 65	X-RAY DIFFRACTION · 1.64 Å	12	0	1	atomic completeness calculated
6XCG · C	NSD2 PWWP1	63 / 65	X-RAY DIFFRACTION · 1.64 Å	4	0	1	atomic completeness calculated
7LMT · A	NSD2 PWWP1	61 / 65	X-RAY DIFFRACTION · 2.27 Å	11	0	2	atomic completeness calculated
7LMT · B	NSD2 PWWP1	61 / 65	X-RAY DIFFRACTION · 2.27 Å	13	0	2	atomic completeness calculated
7LMT · C	NSD2 PWWP1	61 / 65	X-RAY DIFFRACTION · 2.27 Å	13	0	2	atomic completeness calculated
7LMT · D	NSD2 PWWP1	62 / 65	X-RAY DIFFRACTION · 2.27 Å	20	1	2	atomic completeness calculated
7LMT · E	NSD2 PWWP1	62 / 65	X-RAY DIFFRACTION · 2.27 Å	14	0	2	atomic completeness calculated
7LMT · F	NSD2 PWWP1	61 / 65	X-RAY DIFFRACTION · 2.27 Å	11	0	2	atomic completeness calculated
7LMT · G	NSD2 PWWP1	61 / 65	X-RAY DIFFRACTION · 2.27 Å	16	0	2	atomic completeness calculated
7LMT · H	NSD2 PWWP1	61 / 65	X-RAY DIFFRACTION · 2.27 Å	14	0	2	atomic completeness calculated
7MDN · A	NSD2 PWWP1	61 / 65	X-RAY DIFFRACTION · 2.42 Å	11	0	2	atomic completeness calculated
7MDN · B	NSD2 PWWP1	61 / 65	X-RAY DIFFRACTION · 2.42 Å	13	0	2	atomic completeness calculated
7MDN · C	NSD2 PWWP1	61 / 65	X-RAY DIFFRACTION · 2.42 Å	13	0	2	atomic completeness calculated
7MDN · D	NSD2 PWWP1	62 / 65	X-RAY DIFFRACTION · 2.42 Å	20	1	2	atomic completeness calculated
7MDN · E	NSD2 PWWP1	62 / 65	X-RAY DIFFRACTION · 2.42 Å	14	0	2	atomic completeness calculated
7MDN · F	NSD2 PWWP1	61 / 65	X-RAY DIFFRACTION · 2.42 Å	11	0	2	atomic completeness calculated
7MDN · G	NSD2 PWWP1	61 / 65	X-RAY DIFFRACTION · 2.42 Å	16	0	2	atomic completeness calculated
7MDN · H	NSD2 PWWP1	61 / 65	X-RAY DIFFRACTION · 2.42 Å	14	0	2	atomic completeness calculated
7VLN · A	NSD2 PWWP1	60 / 65	X-RAY DIFFRACTION · 3.09 Å	0	0	1	atomic completeness calculated
7VLN · B	NSD2 PWWP1	60 / 65	X-RAY DIFFRACTION · 3.09 Å	0	0	1	atomic completeness calculated
7VLN · C	NSD2 PWWP1	62 / 65	X-RAY DIFFRACTION · 3.09 Å	0	0	0	atomic completeness calculated
9EXW · A	NSD2 PWWP1	65 / 65	X-RAY DIFFRACTION · 2.43 Å	8	0	1	atomic completeness calculated
9EXW · B	NSD2 PWWP1	61 / 65	X-RAY DIFFRACTION · 2.43 Å	4	0	2	atomic completeness calculated
9EXX · A	NSD2 PWWP1	65 / 65	X-RAY DIFFRACTION · 1.943 Å	8	0	1	atomic completeness calculated
9EXX · B	NSD2 PWWP1	61 / 65	X-RAY DIFFRACTION · 1.943 Å	4	0	2	atomic completeness calculated
9EXY · A	NSD2 PWWP1	59 / 65	X-RAY DIFFRACTION · 1.699 Å	4	0	1	atomic completeness calculated
9EXY · B	NSD2 PWWP1	65 / 65	X-RAY DIFFRACTION · 1.699 Å	4	0	1	atomic completeness calculated
9FOC · A	NSD2 PWWP1	65 / 65	X-RAY DIFFRACTION · 1.618 Å	7	0	2	atomic completeness calculated
9FOC · B	NSD2 PWWP1	65 / 65	X-RAY DIFFRACTION · 1.618 Å	11	0	2	atomic completeness calculated
9FOE · A	NSD2 PWWP1	58 / 65	X-RAY DIFFRACTION · 1.963 Å	4	0	1	atomic completeness calculated
9KN9 · A	NSD2 PWWP1	62 / 65	X-RAY DIFFRACTION · 2.0 Å	9	0	1	atomic completeness calculated
9KN9 · B	NSD2 PWWP1	62 / 65	X-RAY DIFFRACTION · 2.0 Å	6	0	1	atomic completeness calculated
9KNA · A	NSD2 PWWP1	62 / 65	X-RAY DIFFRACTION · 2.92 Å	10	0	2	atomic completeness calculated
9KNA · B	NSD2 PWWP1	62 / 65	X-RAY DIFFRACTION · 2.92 Å	9	0	2	atomic completeness calculated
9KNB · A	NSD2 PWWP1	60 / 65	X-RAY DIFFRACTION · 1.84 Å	13	2	1	atomic completeness calculated
9Y60 · A	NSD2 PWWP1	65 / 65	X-RAY DIFFRACTION · 2.023 Å	16	0	1	atomic completeness calculated
9Y61 · A	NSD2 PWWP1	65 / 65	ELECTRON MICROSCOPY · 3.1 Å	0	0	1	atomic completeness calculated

Reproducible scientific exports

Individual experimental mmCIF files are verified by their original SHA-256. Core coordinates, standard heavy-atom templates and source UniProt mappings are analyzed model-by-model. Union-of-alternates and conformer-consistent completeness are distinct; 5 Å and 6 Å geometric proximity are not equivalent to a validated interaction.

NMR and model assessments Ligand environment evidence Contact residue distances Coordinate provenance Calculation manifest