SAXSdb — 7ppb

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Bone morphogenetic protein 10

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 317–424	Not recorded	Bone morphogenetic protein receptor type-2 × 2 （Q13873）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；294.15 K；14% PEG 3350 0.14 M KCl	Resolution 2.40 Å R-free 0.235

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 7PPB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6SF1 Bone morphogenetic protein 10 (BMP10) complexed with extracellular domain of activin receptor-like kinase 1 (ALK1). Deposited 2019-07-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 317–424（108 aa）	Not recorded	NI NICKEL (II) ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；17% PEG 3350, 0.175 M NH4I, 0.1 M HEPES pH 7.8	Resolution 2.80 Å R-free 0.279
6SF3 Bone morphogenetic protein 10 (BMP10) in complex with extracellular domain of activin receptor-like kinase 1 (ALK1) at 2.3 Angstrom Deposited 2019-07-31	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 317–424（108 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.07 M Amino acids (0.014 M DL-Glutamic acids monohydrate; 0.014 M DL-Alanine; 0.014 M Glycine; 0.014 M DL-Lysine monohydrochloride; 0.014 M DL-Serine), 0.07 M Buffer System 3 (0.07 M Tris(base)/BICINE), 35% Precipitant Mix 4 (9% v/v MPD, 9% w/v PEG 1000, 9% w/ PEG3350)	Resolution 2.30 Å R-free 0.243
7POI Prodomain bound BMP10 crystal form 1 Deposited 2021-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 317–424（108 aa） Chain B 317–424（108 aa） Chain C 22–316（295 aa） Chain D 22–316（295 aa）	Not recorded	TAR D(-)-TARTARIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；294.15 K；19% PEG 3350 0.15 M Ammonium tartrate dibasic 0.02 M Sodium cacodylate trihydrate	Resolution 2.90 Å R-free 0.268
7POJ Prodomain bound BMP10 crystal form 2 Deposited 2021-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 317–424（108 aa） Chain B 317–424（108 aa） Chain C 22–316（295 aa） Chain D 22–316（295 aa）	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；294.15 K；20% PEG3350 0.2 M ammonium tartrate dibasic	Resolution 3.50 Å R-free 0.300
7PPA High resolution structure of bone morphogenetic protein receptor type II (BMPRII) extracellular domain in complex with BMP10 Deposited 2021-09-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 317–424（108 aa） Chain B 317–424（108 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；294.15 K；14% PEG 3350 0.19 M Ammonium citrate dibasic 0.02 M Sodium citrate tribasic dihydrate	Resolution 1.48 Å R-free 0.207
7PPC Ternary signalling complex of BMP10 bound to ALK1 and BMPRII Deposited 2021-09-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 317–424（108 aa） Chain B 317–424（108 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294.15 K；20% PEG 3350 0.2 M Calcium acetate hydrate	Resolution 3.60 Å R-free 0.282
7PPC Ternary signalling complex of BMP10 bound to ALK1 and BMPRII Deposited 2021-09-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 317–424（108 aa） Chain D 317–424（108 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294.15 K；20% PEG 3350 0.2 M Calcium acetate hydrate	Resolution 3.60 Å R-free 0.282
9DPY BMP-10 with BMP-9 Crystal Contacts Deposited 2024-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 320–424（105 aa） Chain B 320–424（105 aa）	Mutation：N357F, Y358F, A374T, Y409L, F411Y Mutation：N357F, Y358F, A374T, Y409L, F411Y	PO4 PHOSPHATE ION × 13 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；25% (v/v) 1,2-propanediol, 100 mM sodium phosphate dibasic/potassium phosphate monobasic pH 6.2, 10% (v/v) glycerol	Resolution 1.77 Å R-free 0.251

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BMP10_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–108； UniProt 317–424

Bone morphogenetic protein receptor type-2

Homo sapiens

UniProt Q13873

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 27–150	Not recorded	Bone morphogenetic protein 10 × 2 （O95393）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；294.15 K；14% PEG 3350 0.14 M KCl	Resolution 2.40 Å R-free 0.235

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 7PPB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3G2F Crystal structure of the kinase domain of bone morphogenetic protein receptor type II (BMPR2) at 2.35 A resolution Deposited 2009-01-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 189–517（329 aa） Fragment：UNP residues 189-517, protein kinase domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.3M ammonium_sulfate, 25% w/v PEG 8000, 0.1M Cacodylate pH6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.35 Å R-free 0.246
3G2F Crystal structure of the kinase domain of bone morphogenetic protein receptor type II (BMPR2) at 2.35 A resolution Deposited 2009-01-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 189–517（329 aa） Fragment：UNP residues 189-517, protein kinase domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.3M ammonium_sulfate, 25% w/v PEG 8000, 0.1M Cacodylate pH6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.35 Å R-free 0.246
6UNP Crystal structure of the kinase domain of BMPR2-D485G Deposited 2019-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 188–529（342 aa） Fragment：kinase domain	Mutation：D485G Non-standard monomer：Yes (specific site not provided by mmCIF)	ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 7 SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.1 M Na Cacodylate, pH 6.0, 0.3 M Ammonium sulfate, 22% w/v PEG 8000	Resolution 2.30 Å R-free 0.211
6UNP Crystal structure of the kinase domain of BMPR2-D485G Deposited 2019-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 188–529（342 aa） Fragment：kinase domain	Mutation：D485G Non-standard monomer：Yes (specific site not provided by mmCIF)	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 11 SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.1 M Na Cacodylate, pH 6.0, 0.3 M Ammonium sulfate, 22% w/v PEG 8000	Resolution 2.30 Å R-free 0.211
7PPA High resolution structure of bone morphogenetic protein receptor type II (BMPRII) extracellular domain in complex with BMP10 Deposited 2021-09-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 27–150（124 aa） Chain D 27–150（124 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；294.15 K；14% PEG 3350 0.19 M Ammonium citrate dibasic 0.02 M Sodium citrate tribasic dihydrate	Resolution 1.48 Å R-free 0.207
7PPC Ternary signalling complex of BMP10 bound to ALK1 and BMPRII Deposited 2021-09-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain I 27–150（124 aa） Chain J 27–150（124 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294.15 K；20% PEG 3350 0.2 M Calcium acetate hydrate	Resolution 3.60 Å R-free 0.282
7PPC Ternary signalling complex of BMP10 bound to ALK1 and BMPRII Deposited 2021-09-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain K 27–150（124 aa） Chain L 27–150（124 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294.15 K；20% PEG 3350 0.2 M Calcium acetate hydrate	Resolution 3.60 Å R-free 0.282
7U5O CRYSTAL STRUCTURE OF THE BONE MORPHOGENETIC PROTEIN RECEPTOR TYPE 2 LIGAND BINDING DOMAIN IN COMPLEX WITH ACTIVIN-B Deposited 2022-03-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 27–137（111 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；294 K；175 mM Ammonium Sulfate 100 mM Bis Tris 14% PEG 3000	Resolution 3.45 Å R-free 0.284
7U5O CRYSTAL STRUCTURE OF THE BONE MORPHOGENETIC PROTEIN RECEPTOR TYPE 2 LIGAND BINDING DOMAIN IN COMPLEX WITH ACTIVIN-B Deposited 2022-03-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 27–137（111 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；294 K；175 mM Ammonium Sulfate 100 mM Bis Tris 14% PEG 3000	Resolution 3.45 Å R-free 0.284
7U5O CRYSTAL STRUCTURE OF THE BONE MORPHOGENETIC PROTEIN RECEPTOR TYPE 2 LIGAND BINDING DOMAIN IN COMPLEX WITH ACTIVIN-B Deposited 2022-03-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 27–137（111 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；294 K；175 mM Ammonium Sulfate 100 mM Bis Tris 14% PEG 3000	Resolution 3.45 Å R-free 0.284

5 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BMPR2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–125； UniProt 27–150

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7ppb
Deposition date deposition_date	2021-09-13
Structure title title	2.4 angstrom crystal structure of bone morphogenetic protein receptor type II (BMPRII) extracellular domain in complex with BMP10
Keywords keywords	BMPRII BMP10 TGF-beta ligand and receptor Signalling complex, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	21.28 Å
Radius of gyration Rg (electron density) rg_electron	21.04 Å
Forward intensity I(0) i0	9404940.00
Molecular weight molecular_weight	22373.0 kDa
Excluded volume excluded_volume	27805 Å³
Envelope volume envelope_volume	34363 Å³
Hydration-shell volume shell_volume	15208 Å³
Envelope diameter envelope_diameter	77.9 Å
Shell Rg shell_rg	25.41 Å
Envelope Rg envelope_rg	21.63 Å
Shape Rg shape_rg	21.01 Å
Total Rg total_rg	21.78 Å
Total atoms total_atoms	1564
Residues n_residues	199
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	76.6 Å
Rg (real space) rg_real	21.53 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	9.4050e+06
I(0) uncertainty (real space) i0_real_error	1.3730e+05
Rg (reciprocal space) rg_reciprocal	21.49 Å
I(0) (reciprocal space) i0_reciprocal	9405000.0000
Solution quality estimate total_estimate	0.8043
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.3 Å
Skewness Skewness skewness	0.579
Kurtosis Kurtosis kurtosis	-0.240
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1147000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.653; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.525; Smooth: 0.969

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Bone morphogenetic protein 10
Molecular weight formula_weight	12177.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1602

NAKGNYCKRTPLYIDFKEIGWDSWIIAPPGYEAYECRGVCNYPLAEHLTPTKHAIIQALVHLKNSQKASKACCVPTKLEPISILYLDKGVVTYKFKYEGMAVSECGCR

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Bone morphogenetic protein receptor type-2
Molecular weight formula_weight	13965.4 kDa
EC 编号 ec_number	2.7.11.30
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSQNQERLCAFKDPYQQDLGIGESRISHENGTILCSKGSTCYGLWEKSKGDINLVKQGCWSHIGDPQECHYEECVVTTTPPSIQNGTYRFCCCSTDLCNVNFTENFPPPDTTPLSPPHSFNRDET

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	38

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8. Citations (1)

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Unit-cell length a length_a	119.589 Å
Unit-cell length b length_b	46.343 Å
Unit-cell length c length_c	43.753 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.57 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	42.820 Å
R factor r_factor	0.2076
R_work r_work	0.2061
R_free r_free	0.2347

fit	/app/data/saxs_computation/pp/7ppb/7ppb.fit
pddf	/app/data/pr_computation/pp/7ppb/7ppb.pr.out
profile	/app/data/saxs_computation/pp/7ppb/7ppb.dat

2.4 angstrom crystal structure of bone morphogenetic protein receptor type II (BMPRII) extracellular domain in complex with BMP10

1. Protein Identity and Related Structures Protein Identity & Related Structures

Bone morphogenetic protein 10

State in the Current Structure

Other States of the Same Protein in the Database

Bone morphogenetic protein receptor type-2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)