SAXSdb — 2bm2

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

HUMAN BETA2 TRYPTASE

HOMO SAPIENS

UniProt P20231

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 31–275 Chain B； UniProt 31–275 Chain C； UniProt 31–275 Chain D； UniProt 31–275	Not recorded	PM2 1-[3-(1-{[5-(2-PHENYLETHYL)PYRIDIN-3-YL]CARBONYL}PIPERIDIN-4-YL)PHENYL]METHANAMINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：291 K；PEG 3000 13-19%. NA.ACETATE 100 MM PH 5. T=18 DEG C. TAKES ABOUT 3 DAYS TO GET 200 MICROMETRE SILEX SHAPED CRYSTALS	Resolution 2.20 Å R-free 0.259

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 2BM2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A0L HUMAN BETA-TRYPTASE: A RING-LIKE TETRAMER WITH ACTIVE SITES FACING A CENTRAL PORE Deposited 1997-12-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 31–274（244 aa） Chain B 31–274（244 aa） Chain C 31–274（244 aa） Chain D 31–274（244 aa）	Not recorded	APA (2S)-3-(4-carbamimidoylphenyl)-2-hydroxypropanoic acid × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；pH 5.0	Resolution 3.00 Å R-free 0.276
2FPZ Human tryptase with 2-amino benzimidazole Deposited 2006-01-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 31–275（245 aa） Chain B 31–275（245 aa） Chain C 31–275（245 aa） Chain D 31–275（245 aa）	Not recorded	AX7 1H-benzimidazol-2-amine × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；281 K；0.1M sodium acetate, 0.2M ammonium sulfate, 30% PEG 1500, pH 4.6, VAPOR DIFFUSION, temperature 281K	Resolution 2.00 Å R-free 0.240
2FS8 Human beta-tryptase II with inhibitor CRA-29382 Deposited 2006-01-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 31–275（245 aa） Chain B 31–275（245 aa） Chain C 31–275（245 aa） Chain D 31–275（245 aa）	Not recorded	C3A ALLYL {(1S)-1-[(5-{4-[(2,3-DIHYDRO-1H-INDEN-2-YLAMINO)CARBONYL]BENZYL}-1,2,4-OXADIAZOL-3-YL)CARBONYL]-3-PYRROLIDIN-3-YLPROPYL}CARBAMATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2mg/mL protein in 10mM MES, pH 6.1, 2M NaCl mixed in reservoir solution containing 0.1 M NaOAc, pH 4.6, 0.2 M ammonium sulfate, 30% PEG 1500. Crystallization drops were set up using various ratios of protein solution to crystallization solution. Crystals appropriate for diffraction studies appeared in 2-5 days at room temperature, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.50 Å R-free 0.250
2FS9 Human beta tryptase II with inhibitor CRA-28427 Deposited 2006-01-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 31–275（245 aa） Chain B 31–275（245 aa） Chain C 31–275（245 aa） Chain D 31–275（245 aa）	Not recorded	C4A ETHYL {(1S)-5-AMINO-1-[(5-{4-[(2,3-DIHYDRO-1H-INDEN-2-YLAMINO)CARBONYL]BENZYL}-1,2,4-OXADIAZOL-3-YL)CARBONYL]PENTYL}CARBAMATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2mg/mL protein in 10mM MES, pH 6.1, 2M NaCl mixed with reservoir solution containing 0.1 M NaOAc, pH 4.6, 0.2 M ammonium sulfate, 30% PEG 1500. Crystallization drops were set up using various ratios of protein solution to crystallization solution. Crystals appropriate for diffraction studies appeared in 2-5 days at room temperature, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.30 Å R-free 0.254
2FWW human beta-tryptase II complexed with 4-piperidinebutyrate to make acylenzyme Deposited 2006-02-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 31–275（245 aa） Chain B 31–275（245 aa） Chain C 31–275（245 aa） Chain D 31–275（245 aa）	Not recorded	C1R 4-PIPERIDINEBUTYRATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions 293 K；2mg/mL of protein, 10 mM MES, pH 6.1, 2M NaCl was mixed with crystallization solution 0.1 M NaOAc, pH 4.6, 0.2 M ammonium sulfate, 30% PEG 1500. Crystallization drops were set up using various ratios of protein solution to crystallization solution. Crystals appropriate for diffraction studies appeared in 2-5 days at room temperature, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.25 Å R-free 0.257
2FXR human beta tryptase II complexed with activated ketone inhibitor CRA-29382 Deposited 2006-02-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 31–275（245 aa） Chain B 31–275（245 aa） Chain C 31–275（245 aa） Chain D 31–275（245 aa）	Not recorded	C3A ALLYL {(1S)-1-[(5-{4-[(2,3-DIHYDRO-1H-INDEN-2-YLAMINO)CARBONYL]BENZYL}-1,2,4-OXADIAZOL-3-YL)CARBONYL]-3-PYRROLIDIN-3-YLPROPYL}CARBAMATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2mg/mL protein, 10 mM MES, pH 6.1, 2M NaCl dissolved in 0.1 M NaOAc, pH 4.6, 0.2 M ammonium sulfate, 30% PEG 1500. Crystallization drops were set up using various ratios of protein solution to crystallization solution. Crystals appropriate for diffraction studies appeared in 2-5 days at room temperature, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.50 Å R-free 0.259
2GDD Human beta II tryptase with inhibitor CRA-27592 Deposited 2006-03-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 31–275（245 aa） Chain B 31–275（245 aa） Chain C 31–275（245 aa） Chain D 31–275（245 aa）	Not recorded	5AM BENZYL {(1S)-5-AMINO-1-[(S)-HYDROXY(5-{[4-(4-PHENYLBUTANOYL)PIPERAZIN-1-YL]METHYL}-1,2,4-OXADIAZOL-3-YL)METHYL]PENTYL}CARBAMATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；293 K；Tryptase was purchased from Promega (catalog #G563X). The protein was formulated as a 2 mg/mL solution in 10 mM MES (pH 6.1) and 2M NaCl, and was crystallized from a solution of 0.1 M NaoAc (pH 4.6), 0.2 M ammonium sulfate and 30% PEG 1500 (all reagents obtained from Hampton Research). Crystallization drops were set up at various ratios of protein solution to crystallization solution. Crystals appeared in 2-5 days at room temperature., VAPOR DIFFUSION, temperature 293.0K	Resolution 2.35 Å R-free 0.254
5F03 TRYPTASE B2 IN COMPLEX WITH 5-(3-Aminomethyl-phenoxymethyl)-3-[3-(2-chloro-pyridin-3-ylethynyl)-phenyl]-oxazolidin-2-one; compound with trifluoro-acetic acid Deposited 2015-11-27	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 31–275（245 aa）	Mutation：NO	5TA (5~{S})-5-[[3-(aminomethyl)phenoxy]methyl]-3-[3-[2-(2-chloranylpyridin-3-yl)ethynyl]phenyl]-1,3-oxazolidin-2-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 10000, 0.1 M HEPES	Resolution 1.94 Å R-free 0.200
5F03 TRYPTASE B2 IN COMPLEX WITH 5-(3-Aminomethyl-phenoxymethyl)-3-[3-(2-chloro-pyridin-3-ylethynyl)-phenyl]-oxazolidin-2-one; compound with trifluoro-acetic acid Deposited 2015-11-27	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 31–275（245 aa）	Mutation：NO	5TA (5~{S})-5-[[3-(aminomethyl)phenoxy]methyl]-3-[3-[2-(2-chloranylpyridin-3-yl)ethynyl]phenyl]-1,3-oxazolidin-2-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 10000, 0.1 M HEPES	Resolution 1.94 Å R-free 0.200
9QFU Human Tryptase beta-2 (hTPSB2) complexed with covalent inhibitor Compound #1 Deposited 2025-03-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 31–273（243 aa） Chain B 31–273（243 aa） Chain C 31–273（243 aa） Chain D 31–273（243 aa）	Not recorded	A1I52 ~{N}-[(1~{S},2~{S})-6-azanyl-1-[5-[[4-[2-(3,4-dichlorophenyl)ethoxy]phenyl]methyl]-1,2,4-oxadiazol-3-yl]-1-oxidanyl-hexan-2-yl]-4-fluoranyl-benzamide × 4 SO4 SULFATE ION × 16 PEG DI(HYDROXYETHYL)ETHER × 2 EDO 1,2-ETHANEDIOL × 15 ACT ACETATE ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；The protein was formulated as a 2 mg/mL solution in 10 mM MES (pH 6.1) and 2M NaCl, and was crystallized from a solution of 0.1 M NaoAc (pH 4.6), 0.2 M ammonium sulfate and 30% PEG 1500	Resolution 1.98 Å R-free 0.221
9QFV Human Tryptase beta-2 (hTPSB2) Deposited 2025-03-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 31–275（245 aa） Chain B 31–275（245 aa） Chain C 31–275（245 aa） Chain D 31–275（245 aa）	Not recorded	ACT ACETATE ION × 4 EDO 1,2-ETHANEDIOL × 13 SO4 SULFATE ION × 8 GOL GLYCEROL × 4 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 4 1PE PENTAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；293 K；The protein was formulated as a 2 mg/mL solution in 10 mM MES (pH 6.1) and 2M NaCl, and was crystallized from a solution of 0.1 M NaoAc (pH 4.6), 0.2 M ammonium sulfate and 30% PEG 1500	Resolution 2.06 Å R-free 0.219

10 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TRYB2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–245； UniProt 31–275 Author chain B； PDBConstruct 1–245； UniProt 31–275 Author chain C； PDBConstruct 1–245； UniProt 31–275 Author chain D； PDBConstruct 1–245； UniProt 31–275

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	2bm2
Deposition date deposition_date	2005-03-09
Structure title title	human beta-II tryptase in complex with 4-(3-Aminomethyl-phenyl)- piperidin-1-yl-(5-phenethyl- pyridin-3-yl)-methanone
Keywords keywords	SERINE PROTEASE INHIBITOR, GLYCOPROTEIN, HYDROLASE, POLYMORPHISM, PROTEASE, SERINE PROTEASE; HYDROLASE
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	33.44 Å
Radius of gyration Rg (electron density) rg_electron	32.85 Å
Forward intensity I(0) i0	184821000.00
Molecular weight molecular_weight	109990.0 kDa
Excluded volume excluded_volume	137840 Å³
Envelope volume envelope_volume	176200 Å³
Hydration-shell volume shell_volume	43620 Å³
Envelope diameter envelope_diameter	101.0 Å
Shell Rg shell_rg	41.15 Å
Envelope Rg envelope_rg	31.74 Å
Shape Rg shape_rg	32.85 Å
Total Rg total_rg	33.51 Å
Total atoms total_atoms	7768
Residues n_residues	896
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	102.1 Å
Rg (real space) rg_real	33.28 Å
Rg uncertainty (real space) rg_real_error	0.64 Å
I(0) (real space) i0_real	1.8480e+08
I(0) uncertainty (real space) i0_real_error	2.5600e+06
Rg (reciprocal space) rg_reciprocal	33.38 Å
I(0) (reciprocal space) i0_reciprocal	184800000.0000
Solution quality estimate total_estimate	0.9088
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	50.0 Å
Skewness Skewness skewness	0.032
Kurtosis Kurtosis kurtosis	-0.728
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	50330000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.964

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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	HUMAN BETA2 TRYPTASE
Molecular weight formula_weight	27491.4 kDa
EC 编号 ec_number	3.4.21.59
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8145

IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVKVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPKKP

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	PICHIA PASTORIS

Entity 2 Entity 2 non-polymer

Description description	1-[3-(1-{[5-(2-PHENYLETHYL)PYRIDIN-3-YL]CARBONYL}PIPERIDIN-4-YL)PHENYL]METHANAMINE
Molecular weight formula_weight	399.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	377

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2bm2a_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

Domain ID domain_id	d2bm2b_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

Domain ID domain_id	d2bm2c_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

Domain ID domain_id	d2bm2d_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

CATH v4.4 (8 domains)

Domain ID domain_id	2bm2A01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	2bm2A02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	2bm2B01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	2bm2B02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	2bm2C01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	2bm2C02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	2bm2D01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	2bm2D02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

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8. Citations (1)

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Unit-cell length a length_a	82.000 Å
Unit-cell length b length_b	82.000 Å
Unit-cell length c length_c	171.190 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2030
R_work r_work	0.2030
R_free r_free	0.2590

fit	/app/data/saxs_computation/bm/2bm2/2bm2.fit
pddf	/app/data/pr_computation/bm/2bm2/2bm2.pr.out
profile	/app/data/saxs_computation/bm/2bm2/2bm2.dat

human beta-II tryptase in complex with 4-(3-Aminomethyl-phenyl)- piperidin-1-yl-(5-phenethyl- pyridin-3-yl)-methanone

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

HUMAN BETA2 TRYPTASE

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