SAXSdb — 5iu6

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

Purine nucleoside phosphorylase DeoD-type

Escherichia coli

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 2–238 Chain B； UniProt 2–238 Chain C； UniProt 2–238	Not recorded	7HX 7H-pyrrolo[2,3-d]pyrimidin-4-ol × 6 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：LIQUID DIFFUSION；294 K；AMMONIUM SULPHATE	Resolution 2.51 Å R-free 0.200

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 5IU6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A69 PURINE NUCLEOSIDE PHOSPHORYLASE IN COMPLEX WITH FORMYCIN B AND SULPHATE (PHOSPHATE) Deposited 1998-03-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–238（238 aa） Chain B 1–238（238 aa） Chain C 1–238（238 aa）	Not recorded	SO4 SULFATE ION × 6 FMB FORMYCIN B × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.3；28-35% AMMONIUM SULPHATE, 50 MM CITRATE BUFFER, PH 5.2-5.4, pH 5.3	Resolution 2.10 Å
1ECP PURINE NUCLEOSIDE PHOSPHORYLASE Deposited 1995-07-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–238（238 aa） Chain B 1–238（238 aa） Chain C 1–238（238 aa） Chain D 1–238（238 aa） Chain E 1–238（238 aa） Chain F 1–238（238 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.290
1K9S PURINE NUCLEOSIDE PHOSPHORYLASE FROM E. COLI IN COMPLEX WITH FORMYCIN A DERIVATIVE AND PHOSPHATE Deposited 2001-10-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–237（237 aa） Chain B 1–237（237 aa） Chain C 1–237（237 aa） Chain D 1–237（237 aa） Chain E 1–237（237 aa） Chain F 1–237（237 aa）	Not recorded	PO4 PHOSPHATE ION × 6 FM2 2-(7-AMINO-6-METHYL-3H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL × 3 FM1 2-HYDROXYMETHYL-5-(7-METHYLAMINO-3H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-TETRAHYDRO-FURAN-3,4-DIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；28-35% ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.184
1OTX Purine Nucleoside Phosphorylase M64V mutant Deposited 2003-03-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–238（238 aa） Chain B 1–238（238 aa） Chain C 1–238（238 aa）	Mutation：M64V Mutation：M64V Mutation：M64V	PO4 PHOSPHATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；295 K；50mM sodium citrate, 30%ammonium sulfate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.70 Å R-free 0.247
1OTY Native PNP +ALLO Deposited 2003-03-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–238（238 aa） Chain B 1–238（238 aa） Chain C 1–238（238 aa）	Not recorded	PO4 PHOSPHATE ION × 6 6MP 6-METHYLPURINE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；295 K；50mM sodium citrate, 30% ammonium sulfate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.236
1OU4 Native PNP +Talo Deposited 2003-03-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–238（238 aa） Chain B 1–238（238 aa） Chain C 1–238（238 aa）	Not recorded	PO4 PHOSPHATE ION × 6 6MP 6-METHYLPURINE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；295 K；50mM sodium Citrate, 30% ammonium sulfate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.244
1OUM M64V PNP +Talo Deposited 2003-03-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–238（238 aa） Chain B 1–238（238 aa） Chain C 1–238（238 aa）	Mutation：M64V Mutation：M64V Mutation：M64V	TAL 9-(6-DEOXY-ALPHA-L-TALOFURANOSYL)-6-METHYLPURINE × 6 PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；295 K；50mM sodium citrate, 30% ammonium sulfate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.40 Å R-free 0.260
1OV6 M64V PNP + ALLO Deposited 2003-03-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–238（238 aa） Fragment：Purine Nuleoside Phosphorylase Chain B 1–238（238 aa） Fragment：Purine Nuleoside Phosphorylase Chain C 1–238（238 aa） Fragment：Purine Nuleoside Phosphorylase	Mutation：M64V Mutation：M64V Mutation：M64V	PO4 PHOSPHATE ION × 6 DBM 9-(6-DEOXY-BETA-D-ALLOFURANOSYL)-6-METHYLPURINE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；295 K；50mM sodium citrate, 30% ammonium sulfate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.40 Å R-free 0.258
1OVG M64V PNP +MePdr Deposited 2003-03-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–238（238 aa） Chain B 1–238（238 aa） Chain C 1–238（238 aa）	Mutation：M64V Mutation：M64V Mutation：M64V	PO4 PHOSPHATE ION × 6 MDR 9-(2-DEOXY-BETA-D-RIBOFURANOSYL)-6-METHYLPURINE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；295 K；50mM sodium citrate, 30% ammonium sulfate , pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.20 Å R-free 0.259
3UT6 Crystal structure of E. Coli PNP complexed with PO4 and formycin A Deposited 2011-11-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–238（237 aa） Chain B 2–238（237 aa） Chain C 2–238（237 aa）	Not recorded	FMC (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol × 6 PO4 PHOSPHATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 5.2；291 K；50mM citrate buffer, 35% ammonium phosphate (w/v), pH 5.2, hanging drop, temperature 291K	Resolution 1.90 Å R-free 0.187
4TTI Crystal structure of double mutant E. Coli purine nucleoside phosphorylase with 4 FMC molecules Deposited 2014-06-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: Hexameric	Chain A 2–238（237 aa） Chain B 2–238（237 aa） Chain C 2–238（237 aa） Chain D 2–238（237 aa） Chain E 2–238（237 aa） Chain F 2–238（237 aa）	Not recorded	FMC (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol × 4 PO4 PHOSPHATE ION × 6 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；50 mM citric buffer, 34 % ammonium sulphate	Resolution 1.89 Å R-free 0.210
4TTJ Crystal structure of double mutant E. Coli purine nucleoside phosphorylase with 6 FMC molecules Deposited 2014-06-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: Hexameric	Chain A 2–238（237 aa） Chain B 2–238（237 aa） Chain D 2–238（237 aa）	Not recorded	PO4 PHOSPHATE ION × 6 FMC (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol × 6 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；50 mM citric buffer, 32 % ammonium sulphate	Resolution 1.87 Å R-free 0.194
6XZ2 Crystal structure of E. Coli purine nucleoside phosphorylase mutant Y160W with SO4 and Formycin A Deposited 2020-01-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–238（237 aa） Chain B 2–238（237 aa） Chain C 2–238（237 aa）	Mutation：Y160W Mutation：Y160W Mutation：Y160W	SO4 SULFATE ION × 6 FMC (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；50 mM citrate buffer pH 5.2, 14 % ammonium sulphate (w/v)	Resolution 1.65 Å R-free 0.192
6XZ2 Crystal structure of E. Coli purine nucleoside phosphorylase mutant Y160W with SO4 and Formycin A Deposited 2020-01-31	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–238（237 aa） Chain B 2–238（237 aa） Chain C 2–238（237 aa）	Mutation：Y160W Mutation：Y160W Mutation：Y160W	SO4 SULFATE ION × 3 FMC (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；50 mM citrate buffer pH 5.2, 14 % ammonium sulphate (w/v)	Resolution 1.65 Å R-free 0.192
9FPE Wild type Purine Nucleoside Phosphorylase from E.coli in complex with N2,3-etheno-2-aminopurine Deposited 2024-06-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–239（239 aa） Chain B 1–239（239 aa） Chain C 1–239（239 aa）	Not recorded	GOL GLYCEROL × 6 A1IEC N,2,3-etheno-2-aminopurine × 6 PO4 PHOSPHATE ION × 6 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；Citrate buffer pH 5.2, amonium sulphate 15% w/v	Resolution 1.35 Å R-free 0.213
9FXE D204N mutant of Purine Nucleoside Phosphorylase from E.coli in complex with N2,3-etheno-2-aminopurine Deposited 2024-07-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–239（239 aa） Chain B 1–239（239 aa） Chain C 1–239（239 aa）	Not recorded	PO4 PHOSPHATE ION × 6 A1IEC N,2,3-etheno-2-aminopurine × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；Citrate buffer pH 5.2, amonium sulphate 24% w/v	Resolution 2.12 Å R-free 0.233

15 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DEOD_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–237； UniProt 2–238 Author chain B； PDBConstruct 1–237； UniProt 2–238 Author chain C； PDBConstruct 1–237； UniProt 2–238

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	5iu6
Deposition date deposition_date	2016-03-17
Structure title title	Crystal structure of E.coli purine nucleoside phosphorylase with 7-deazahypoxanthine
Keywords keywords	complex, transferase; TRANSFERASE
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	33.97 Å
Radius of gyration Rg (electron density) rg_electron	33.55 Å
Forward intensity I(0) i0	97374000.00
Molecular weight molecular_weight	77693.0 kDa
Excluded volume excluded_volume	96967 Å³
Envelope volume envelope_volume	128890 Å³
Hydration-shell volume shell_volume	33437 Å³
Envelope diameter envelope_diameter	99.1 Å
Shell Rg shell_rg	38.84 Å
Envelope Rg envelope_rg	32.59 Å
Shape Rg shape_rg	33.56 Å
Total Rg total_rg	33.94 Å
Total atoms total_atoms	5436
Residues n_residues	711
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	99.5 Å
Rg (real space) rg_real	33.85 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	9.7370e+07
I(0) uncertainty (real space) i0_real_error	1.4740e+06
Rg (reciprocal space) rg_reciprocal	33.93 Å
I(0) (reciprocal space) i0_reciprocal	97380000.0000
Solution quality estimate total_estimate	0.8877
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	55.0 Å
Skewness Skewness skewness	-0.017
Kurtosis Kurtosis kurtosis	-0.914
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	21860000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.843

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Purine nucleoside phosphorylase DeoD-type
Molecular weight formula_weight	25721.6 kDa
EC 编号 ec_number	2.4.2.1
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	5593

ATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISVMGHGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIRFKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVEMEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVLLGDK

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	7H-pyrrolo[2,3-d]pyrimidin-4-ol
Molecular weight formula_weight	135.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	137

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5iu6a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
Family Family family	c.56.2.1 — Purine and uridine phosphorylases

Domain ID domain_id	d5iu6b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
Family Family family	c.56.2.1 — Purine and uridine phosphorylases

Domain ID domain_id	d5iu6c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
Family Family family	c.56.2.1 — Purine and uridine phosphorylases

CATH v4.4 (3 domains)

Domain ID domain_id	5iu6A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

Domain ID domain_id	5iu6B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

Domain ID domain_id	5iu6C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

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8. Citations (1)

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Unit-cell length a length_a	120.370 Å
Unit-cell length b length_b	120.370 Å
Unit-cell length c length_c	238.971 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.510 Å
Low-resolution limit resolution_low	29.860 Å
R factor r_factor	0.1570
R_work r_work	0.1547
R_free r_free	0.2005

fit	/app/data/saxs_computation/iu/5iu6/5iu6.fit
pddf	/app/data/pr_computation/iu/5iu6/5iu6.pr.out
profile	/app/data/saxs_computation/iu/5iu6/5iu6.dat

Crystal structure of E.coli purine nucleoside phosphorylase with 7-deazahypoxanthine

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

Purine nucleoside phosphorylase DeoD-type

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