SAXSdb — 5vde

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

Metal homeostasis factor ATX1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–73 Chain B； UniProt 1–73	Not recorded	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；0.1 M HEPES (pH 7.3), 24% (W/v) PEG3350	Resolution 1.65 Å R-free 0.206
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–73 Chain D； UniProt 1–73	Not recorded	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；0.1 M HEPES (pH 7.3), 24% (W/v) PEG3350	Resolution 1.65 Å R-free 0.206
3	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–73 Chain B； UniProt 1–73 Chain C； UniProt 1–73 Chain D； UniProt 1–73	Not recorded	CU1 COPPER (I) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；0.1 M HEPES (pH 7.3), 24% (W/v) PEG3350	Resolution 1.65 Å R-free 0.206

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 5VDE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CC7 CRYSTAL STRUCTURE OF THE ATX1 METALLOCHAPERONE PROTEIN Deposited 1999-03-04	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 1–73（73 aa）	Not recorded	BEN BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 1.20 Å R-free 0.211
1CC8 CRYSTAL STRUCTURE OF THE ATX1 METALLOCHAPERONE PROTEIN Deposited 1999-03-04	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 1–73（73 aa）	Not recorded	HG MERCURY (II) ION × 1 BEN BENZAMIDINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 1.02 Å R-free 0.172
1FD8 SOLUTION STRUCTURE OF THE CU(I) FORM OF THE YEAST METALLOCHAPERONE, ATX1 Deposited 2000-07-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–73（73 aa）	Not recorded	CU1 COPPER (I) ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM phosphate；Pressure ambient NMR sample composition 1.8mM Cu(I)-Atx1 15N; 100mM phosphate buffer NA; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
1FES SOLUTION STRUCTURE OF THE APO FORM OF THE YEAST METALLOCHAPERONE, ATX1 Deposited 2000-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–73（73 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM phosphate；Pressure ambient NMR sample composition 1.8mM Apo-Atx1 15N; 100mM phosphate buffer NA; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2GGP Solution structure of the Atx1-Cu(I)-Ccc2a complex Deposited 2006-03-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–73（73 aa） Fragment：HMA domain, residues 1-73	Not recorded	CU1 COPPER (I) ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100 mM KPi；Pressure ambient NMR sample composition 1mM Atx1 U-15N,13C, 1mM Ccc2a unlabeled, 1mM Cu(I), 100mM KPi, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
3K7R Crystal structure of [TM][CuAtx1]3 Deposited 2009-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–73（73 aa） Chain B 1–73（73 aa） Chain C 1–73（73 aa）	Not recorded	CU COPPER (II) ION × 4 4SM TETRATHIOMOLYBDATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；287 K；0.15 M DL-Malic acid, pH 7.0, 20% PEG 3350, EVAPORATION, temperature 287K	Resolution 2.28 Å R-free 0.256
3K7R Crystal structure of [TM][CuAtx1]3 Deposited 2009-10-13	Different construct 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 D 1–73（73 aa） Chain E 1–73（73 aa） Chain F 1–73（73 aa）	Not recorded	CU COPPER (II) ION × 4 4SM TETRATHIOMOLYBDATE × 1 MLT D-MALATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；287 K；0.15 M DL-Malic acid, pH 7.0, 20% PEG 3350, EVAPORATION, temperature 287K	Resolution 2.28 Å R-free 0.256
3K7R Crystal structure of [TM][CuAtx1]3 Deposited 2009-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain G 1–73（73 aa） Chain H 1–73（73 aa） Chain I 1–73（73 aa）	Not recorded	CU COPPER (II) ION × 4 4SM TETRATHIOMOLYBDATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；287 K；0.15 M DL-Malic acid, pH 7.0, 20% PEG 3350, EVAPORATION, temperature 287K	Resolution 2.28 Å R-free 0.256
3K7R Crystal structure of [TM][CuAtx1]3 Deposited 2009-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain J 1–73（73 aa） Chain K 1–73（73 aa） Chain L 1–73（73 aa）	Not recorded	CU COPPER (II) ION × 4 4SM TETRATHIOMOLYBDATE × 1 MLT D-MALATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；287 K；0.15 M DL-Malic acid, pH 7.0, 20% PEG 3350, EVAPORATION, temperature 287K	Resolution 2.28 Å R-free 0.256
3K7R Crystal structure of [TM][CuAtx1]3 Deposited 2009-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–73（73 aa） Chain B 1–73（73 aa） Chain C 1–73（73 aa） Chain D 1–73（73 aa） Chain E 1–73（73 aa） Chain F 1–73（73 aa）	Not recorded	CU COPPER (II) ION × 8 4SM TETRATHIOMOLYBDATE × 2 MLT D-MALATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；287 K；0.15 M DL-Malic acid, pH 7.0, 20% PEG 3350, EVAPORATION, temperature 287K	Resolution 2.28 Å R-free 0.256
3K7R Crystal structure of [TM][CuAtx1]3 Deposited 2009-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 1–73（73 aa） Chain H 1–73（73 aa） Chain I 1–73（73 aa） Chain J 1–73（73 aa） Chain K 1–73（73 aa） Chain L 1–73（73 aa）	Not recorded	CU COPPER (II) ION × 8 4SM TETRATHIOMOLYBDATE × 2 MLT D-MALATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；287 K；0.15 M DL-Malic acid, pH 7.0, 20% PEG 3350, EVAPORATION, temperature 287K	Resolution 2.28 Å R-free 0.256
5VDF Crystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form II Deposited 2017-04-02	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–73（73 aa） Chain B 1–73（73 aa）	Not recorded	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；0.1 M HEPES (pH 7.9), 20% (w/v) PEG3350	Resolution 1.93 Å R-free 0.242
5VDF Crystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form II Deposited 2017-04-02	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–73（73 aa） Chain D 1–73（73 aa）	Not recorded	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；0.1 M HEPES (pH 7.9), 20% (w/v) PEG3350	Resolution 1.93 Å R-free 0.242
5VDF Crystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form II Deposited 2017-04-02	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–73（73 aa） Chain F 1–73（73 aa）	Not recorded	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；0.1 M HEPES (pH 7.9), 20% (w/v) PEG3350	Resolution 1.93 Å R-free 0.242
5VDF Crystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form II Deposited 2017-04-02	Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 1–73（73 aa） Chain H 1–73（73 aa）	Not recorded	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；0.1 M HEPES (pH 7.9), 20% (w/v) PEG3350	Resolution 1.93 Å R-free 0.242
5VDF Crystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form II Deposited 2017-04-02	Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–73（73 aa） Chain B 1–73（73 aa）	Not recorded	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；0.1 M HEPES (pH 7.9), 20% (w/v) PEG3350	Resolution 1.93 Å R-free 0.242
5VDF Crystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form II Deposited 2017-04-02	Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–73（73 aa） Chain D 1–73（73 aa）	Not recorded	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；0.1 M HEPES (pH 7.9), 20% (w/v) PEG3350	Resolution 1.93 Å R-free 0.242
5VDF Crystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form II Deposited 2017-04-02	Different experimental conditions Different structure-quality metrics	Assembly 7 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 1–73（73 aa） Chain H 1–73（73 aa）	Not recorded	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；0.1 M HEPES (pH 7.9), 20% (w/v) PEG3350	Resolution 1.93 Å R-free 0.242

7 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ATX1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–73； UniProt 1–73 Author chain B； PDBConstruct 1–73； UniProt 1–73 Author chain C； PDBConstruct 1–73； UniProt 1–73 Author chain D； PDBConstruct 1–73； UniProt 1–73

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	5vde
Deposition date deposition_date	2017-04-02
Structure title title	Crystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form I
Keywords keywords	Atx1, metallochaperone, copper transfer, metal-binding domain, ferredoxin-like fold, METAL BINDING PROTEIN; METAL BINDING 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	22.24 Å
Radius of gyration Rg (electron density) rg_electron	20.94 Å
Forward intensity I(0) i0	16335900.00
Molecular weight molecular_weight	32152.0 kDa
Excluded volume excluded_volume	41001 Å³
Envelope volume envelope_volume	48521 Å³
Hydration-shell volume shell_volume	19555 Å³
Envelope diameter envelope_diameter	69.8 Å
Shell Rg shell_rg	27.14 Å
Envelope Rg envelope_rg	20.69 Å
Shape Rg shape_rg	20.90 Å
Total Rg total_rg	21.95 Å
Total atoms total_atoms	2246
Residues n_residues	284
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	69.0 Å
Rg (real space) rg_real	22.14 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	1.6340e+07
I(0) uncertainty (real space) i0_real_error	2.0740e+05
Rg (reciprocal space) rg_reciprocal	22.16 Å
I(0) (reciprocal space) i0_reciprocal	16340000.0000
Solution quality estimate total_estimate	0.9047
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	32.4 Å
Skewness Skewness skewness	0.064
Kurtosis Kurtosis kurtosis	-0.726
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6837000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.983

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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	Metal homeostasis factor ATX1
Molecular weight formula_weight	8232.6 kDa
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	2527

MAEIKHYQFNVVMTCSGCSGAVNKVLTKLEPDVSKIDISLEKQLVDVYTTLPYDFILEKIKKTGKEVRSGKQL

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	COPPER (I) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	228

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5vdea_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.17 — HMA, heavy metal-associated domain
Family Family family	d.58.17.1 — HMA, heavy metal-associated domain

Domain ID domain_id	d5vdeb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.17 — HMA, heavy metal-associated domain
Family Family family	d.58.17.1 — HMA, heavy metal-associated domain

Domain ID domain_id	d5vdec_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.17 — HMA, heavy metal-associated domain
Family Family family	d.58.17.1 — HMA, heavy metal-associated domain

Domain ID domain_id	d5vded_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.17 — HMA, heavy metal-associated domain
Family Family family	d.58.17.1 — HMA, heavy metal-associated domain

CATH v4.4 (4 domains)

Domain ID domain_id	5vdeA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	5vdeB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	5vdeC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	5vdeD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

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8. Citations (1)

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Unit-cell length a length_a	35.976 Å
Unit-cell length b length_b	80.054 Å
Unit-cell length c length_c	50.763 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.91 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1659
R_work r_work	0.1637
R_free r_free	0.2059

fit	/app/data/saxs_computation/vd/5vde/5vde.fit
pddf	/app/data/pr_computation/vd/5vde/5vde.pr.out
profile	/app/data/saxs_computation/vd/5vde/5vde.dat

Crystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form I

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

Metal homeostasis factor ATX1

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