SAXSdb — 1ukp

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

Beta-amylase

Glycine max

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–495	Mutation：D374Y / L481R / P487D / K462S	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.10 Å R-free 0.234
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–495	Mutation：D374Y / L481R / P487D / K462S	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.10 Å R-free 0.234
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–495	Mutation：D374Y / L481R / P487D / K462S	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.10 Å R-free 0.234
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1–495	Mutation：D374Y / L481R / P487D / K462S	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.10 Å R-free 0.234

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 1UKP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BFN BETA-AMYLASE/BETA-CYCLODEXTRIN COMPLEX Deposited 1998-05-22	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–495（495 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.4；277 K；49% (NH4)2SO4, 0.1M NAOAC PH 5.4, 18MM 2-MERCAPTOETHANOL, AT 277K	Resolution 2.07 Å R-free 0.211
1BTC THREE-DIMENSIONAL STRUCTURE OF SOYBEAN BETA-AMYLASE DETERMINED AT 3.0 ANGSTROMS RESOLUTION: PRELIMINARY CHAIN TRACING OF THE COMPLEX WITH ALPHA-CYCLODEXTRIN Deposited 1993-02-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 5–495（491 aa）	Not recorded	SO4 SULFATE ION × 1 BME BETA-MERCAPTOETHANOL × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1BYA CRYSTAL STRUCTURES OF SOYBEAN BETA-AMYLASE REACTED WITH BETA-MALTOSE AND MALTAL: ACTIVE SITE COMPONENTS AND THEIR APPARENT ROLE IN CATALYSIS Deposited 1994-01-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–495（495 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1BYB CRYSTAL STRUCTURES OF SOYBEAN BETA-AMYLASE REACTED WITH BETA-MALTOSE AND MALTAL: ACTIVE SITE COMPONENTS AND THEIR APPARENT ROLE IN CATALYSIS Deposited 1994-01-25	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–495（495 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1BYC CRYSTAL STRUCTURES OF SOYBEAN BETA-AMYLASE REACTED WITH BETA-MALTOSE AND MALTAL: ACTIVE SITE COMPONENTS AND THEIR APPARENT ROLE IN CATALYSIS Deposited 1994-01-25	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–495（495 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1BYD CRYSTAL STRUCTURES OF SOYBEAN BETA-AMYLASE REACTED WITH BETA-MALTOSE AND MALTAL: ACTIVE SITE COMPONENTS AND THEIR APPARENT ROLE IN CATALYSIS Deposited 1994-01-25	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–495（495 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1UKO Crystal structure of soybean beta-amylase mutant substituted at surface region Deposited 2003-08-30	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–495（495 aa）	Mutation：D374Y / L481R / P487D	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.241
1UKO Crystal structure of soybean beta-amylase mutant substituted at surface region Deposited 2003-08-30	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–495（495 aa）	Mutation：D374Y / L481R / P487D	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.241
1UKO Crystal structure of soybean beta-amylase mutant substituted at surface region Deposited 2003-08-30	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–495（495 aa）	Mutation：D374Y / L481R / P487D	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.241
1UKO Crystal structure of soybean beta-amylase mutant substituted at surface region Deposited 2003-08-30	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–495（495 aa）	Mutation：D374Y / L481R / P487D	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.241
1V3H The roles of Glu186 and Glu380 in the catalytic reaction of soybean beta-amylase Deposited 2003-11-02	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–495（495 aa）	Mutation：F76L, E186Q	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.60 Å R-free 0.181
1V3I The roles of Glu186 and Glu380 in the catalytic reaction of soybean beta-amylase Deposited 2003-11-02	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–495（495 aa）	Mutation：F76L, E380Q	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.193
1WDP The role of an inner loop in the catalytic mechanism of soybean beta-amylase Deposited 2004-05-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–495（495 aa）	Not recorded	SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.27 Å R-free 0.174
1WDQ The role of an inner loop in the catalytic mechanism of soybean beta-amylase Deposited 2004-05-17	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–495（495 aa）	Mutation：T342V	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.28 Å R-free 0.174
1WDR The role of an inner loop in the catalytic mechanism of soybean beta-amylase Deposited 2004-05-17	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–495（495 aa）	Mutation：T342S Non-standard monomer：Yes (specific site not provided by mmCIF)	GLC alpha-D-glucopyranose × 1 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.35 Å R-free 0.172
1WDS The role of an inner loop in the catalytic mechanism of soybean beta-amylase Deposited 2004-05-17	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–495（495 aa）	Mutation：T342A	GLC alpha-D-glucopyranose × 1 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.64 Å R-free 0.200

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

View Construct and Data Evidence

UniProt name	AMYB_SOYBN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–495； UniProt 1–495 Author chain B； PDBConstruct 1–495； UniProt 1–495 Author chain C； PDBConstruct 1–495； UniProt 1–495 Author chain D； PDBConstruct 1–495； UniProt 1–495

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	1ukp
Deposition date deposition_date	2003-08-31
Structure title title	Crystal structure of soybean beta-amylase mutant substituted at surface region
Keywords keywords	(alpha/beta)8 barrel, hydrolase; 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	44.47 Å
Radius of gyration Rg (electron density) rg_electron	44.09 Å
Forward intensity I(0) i0	736306000.00
Molecular weight molecular_weight	223920.0 kDa
Excluded volume excluded_volume	279620 Å³
Envelope volume envelope_volume	358090 Å³
Hydration-shell volume shell_volume	67952 Å³
Envelope diameter envelope_diameter	160.6 Å
Shell Rg shell_rg	48.70 Å
Envelope Rg envelope_rg	43.43 Å
Shape Rg shape_rg	44.08 Å
Total Rg total_rg	44.30 Å
Total atoms total_atoms	15780
Residues n_residues	1960
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	153.3 Å
Rg (real space) rg_real	44.54 Å
Rg uncertainty (real space) rg_real_error	1.88 Å
I(0) (real space) i0_real	7.3630e+08
I(0) uncertainty (real space) i0_real_error	1.3250e+07
Rg (reciprocal space) rg_reciprocal	44.47 Å
I(0) (reciprocal space) i0_reciprocal	736200000.0000
Solution quality estimate total_estimate	0.8673
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	52.5 Å
Skewness Skewness skewness	0.374
Kurtosis Kurtosis kurtosis	-0.297
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	186700000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.832; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.819

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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	Beta-amylase
Molecular weight formula_weight	56033.2 kDa
EC 编号 ec_number	3.2.1.2
Mutation mutation	D374Y / L481R / P487D / K462S
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	16785

ATSDSNMLLNYVPVYVMLPLGVVNVDNVFEDPDGLKEQLLQLRAAGVDGVMVDVWWGIIELKGPKQYDWRAYRSLLQLVQECGLTLQAIMSFHQCGGNVGDIVNIPIPQWVLDIGESNHDIFYTNRSGTRNKEYLTVGVDNEPIFHGRTAIEIYSDYMKSFRENMSDFLESGLIIDIEVGLGPAGELRYPSYPQSQGWEFPGIGEFQCYDKYLKADFKAAVARAGHPEWELPDDAGKYNDVPESTGFFKSNGTYVTEKGKFFLTWYSNKLLNHGDQILDEANKAFLGCKVKLAIKVSGIHWWYKVENHAAELTAGYYNLNDRDGYRPIARMLSRHHAILNFTCLEMRDSEQPSDAKSGPQELVQQVLSGGWREYIRVAGENALPRYDATAYNQIILNARPQGVNNNGPPKLSMFGVTYLRLSDDLLQKSNFNIFKKFVLKMHADQDYCANPQKYNHAITPLSPSAPKIPIEVLLEATKPTRPFPWLDETDMKVDG

来源 Source

来源生物 organism	Glycine max
通用名 common_name	soybean
NCBI Class编号 ncbi_taxonomy_id	3847
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	20

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1005

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1ukpa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.1 — Amylase, catalytic domain

Domain ID domain_id	d1ukpb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.1 — Amylase, catalytic domain

Domain ID domain_id	d1ukpc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.1 — Amylase, catalytic domain

Domain ID domain_id	d1ukpd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.1 — Amylase, catalytic domain

CATH v4.4 (4 domains)

Domain ID domain_id	1ukpA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	1ukpB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	1ukpC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	1ukpD00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

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8. Citations (1)

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Unit-cell length a length_a	75.463 Å
Unit-cell length b length_b	78.801 Å
Unit-cell length c length_c	88.560 Å
Unit-cell angle α angle_alpha	89.92 °
Unit-cell angle β angle_beta	90.21 °
Unit-cell angle γ angle_gamma	89.90 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2000
R_work r_work	0.2000
R_free r_free	0.2340

fit	/app/data/saxs_computation/uk/1ukp/1ukp.fit
pddf	/app/data/pr_computation/uk/1ukp/1ukp.pr.out
profile	/app/data/saxs_computation/uk/1ukp/1ukp.dat

Crystal structure of soybean beta-amylase mutant substituted at surface region

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

Beta-amylase

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