SAXSdb — 3ps5

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

Tyrosine-protein phosphatase non-receptor type 6

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–595	Mutation：C453S	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；278 K；2.5 ul of SHP-1 at 3.5 mg/ml in 25mM Tris-HCl, beta-mercaptoethanol, 1mM EDTA mixed with 2.5 ul of 1.8M ammonium sulfate, 0.1M glycine, 0.1M Tris-HCl, with the addition of 0.5 ul 14mM deoxy Big Chap to form the final drop., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 3.10 Å R-free 0.276
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–595	Mutation：C453S	SO4 SULFATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；278 K；2.5 ul of SHP-1 at 3.5 mg/ml in 25mM Tris-HCl, beta-mercaptoethanol, 1mM EDTA mixed with 2.5 ul of 1.8M ammonium sulfate, 0.1M glycine, 0.1M Tris-HCl, with the addition of 0.5 ul 14mM deoxy Big Chap to form the final drop., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 3.10 Å R-free 0.276

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 3PS5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FPR CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN THE CATALYTIC DOMAIN OF SHP-1 AND AN IN VITRO PEPTIDE SUBSTRATE PY469 DERIVED FROM SHPS-1. Deposited 2000-08-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 243–526（284 aa） Fragment：CATALYTIC DOMAIN	Mutation：C455S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；ammonium sulfate, pH 8.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.50 Å R-free 0.303
1FPR CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN THE CATALYTIC DOMAIN OF SHP-1 AND AN IN VITRO PEPTIDE SUBSTRATE PY469 DERIVED FROM SHPS-1. Deposited 2000-08-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 243–526（284 aa） Fragment：CATALYTIC DOMAIN	Mutation：C455S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；ammonium sulfate, pH 8.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.50 Å R-free 0.303
1GWZ CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THE PROTEIN TYROSINE PHOSPHATASE SHP-1 Deposited 1998-08-22	Different construct 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 243–541（299 aa） Fragment：CATALYTIC DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.50 Å R-free 0.293
1X6C Solution structures of the SH2 domain of human protein-tyrosine phosphatase SHP-1 Deposited 2005-05-17	Different construct Different mutation/modification 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 110–214（105 aa） Fragment：SH2 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1mM SH2 domain U-15N, 13C; 20mM d-Tris HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2B3O Crystal structure of human tyrosine phosphatase SHP-1 Deposited 2005-09-20	Different construct 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 1–532（532 aa） Fragment：SHP-1	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 800, DTT, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.296
2RMX Solution structure of the SHP-1 C-terminal SH2 domain complexed with a tyrosine-phosphorylated peptide from NKG2A Deposited 2007-11-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 110–214（105 aa） Fragment：SH2 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；Ionic strength (raw mmCIF value) 120；Pressure ambient NMR sample composition 0.8mM [U-13C; U-15N] SHP-1 C-terminal SH2 domain; 0.8mM tyrosine-phosphorylated peptide; 20mM [U-2H] TRIS; 100mM sodium chloride; 0.02% sodium azide; 1mM [U-2H] DTT; 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2YU7 Solution structure of the SHP-1 C-terminal SH2 domain complexed with a tyrosine-phosphorylated peptide from NKG2A Deposited 2007-04-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 110–214（105 aa） Fragment：SH2 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 0.89mM SHP1 SH2 domain U-15N,13C; 0.89mM NKG2A peptide; 20mM d-Tris-HCl (pH 7.4); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
4GRY Crystal structure of SHP1 catalytic domain with SO4 Deposited 2012-08-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 243–528（286 aa） Fragment：Phosphatase domain UNP Residues 242-528	Mutation：C453S	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M MES pH 6.5, 1.5 M ammonium sulfate, 3% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.231
4GRZ Crystal structure of SHP1 catalytic domain with PO4 Deposited 2012-08-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 243–528（286 aa） Fragment：Phosphatase domain UNP Residues 242-528	Mutation：C453S	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.2 M ammonium phosphate, 12% PEG2000 , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.37 Å R-free 0.189
4GS0 Crystal structure of SHP1 catalytic domain with JAK1 activation loop peptide Deposited 2012-08-27	Different construct 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 243–528（286 aa） Fragment：Phosphatase domain (UNP Residues 242-528)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2 M calcium acetate, 13% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.195
4GS0 Crystal structure of SHP1 catalytic domain with JAK1 activation loop peptide Deposited 2012-08-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 243–528（286 aa） Fragment：Phosphatase domain (UNP Residues 242-528)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2 M calcium acetate, 13% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.195
4HJP SHP-1 catalytic domain WPD loop open Deposited 2012-10-13	Different construct 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 243–528（286 aa） Fragment：Phosphatase domain (UNP Residues 242-528)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5, 1.0 M tri-sodium citrate, 2-4% 1-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.40 Å R-free 0.186
4HJQ SHP-1 catalytic domain WPD loop closed Deposited 2012-10-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 243–528（286 aa） Fragment：Phosphatase domain (UNP Residues 242-528)	Mutation：C453S	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH7.5, 20 mM MgCl2, 28% sodium polyacrylate 5100 , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.202
4HJQ SHP-1 catalytic domain WPD loop closed Deposited 2012-10-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 243–528（286 aa） Fragment：Phosphatase domain (UNP Residues 242-528)	Mutation：C453S	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH7.5, 20 mM MgCl2, 28% sodium polyacrylate 5100 , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.202
6SM5 MbC/SHP1-C-SH2 complex Deposited 2019-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 100–214（115 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M sodium citrate tribasic, 0.1 M bistros propane 8.4 and 20 % PEG 3350	Resolution 2.75 Å R-free 0.276
8YHI The Crystal Structure of SHP1 from Biortus. Deposited 2024-02-28	Different construct 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 243–528（286 aa）	Not recorded	SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Hepes pH7.5, 2% PEG 400, 2.0M (NH4)2SO4	Resolution 1.75 Å R-free 0.227

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

View Construct and Data Evidence

UniProt name	PTN6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–595； UniProt 1–595

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	3ps5
Deposition date deposition_date	2010-11-30
Structure title title	Crystal structure of the full-length Human Protein Tyrosine Phosphatase SHP-1
Keywords keywords	SH2, PTP, Phosphatase, HYDROLASE, SIGNALING PROTEIN; HYDROLASE, 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	27.58 Å
Radius of gyration Rg (electron density) rg_electron	26.61 Å
Forward intensity I(0) i0	64114700.00
Molecular weight molecular_weight	60402.0 kDa
Excluded volume excluded_volume	74792 Å³
Envelope volume envelope_volume	95009 Å³
Hydration-shell volume shell_volume	30061 Å³
Envelope diameter envelope_diameter	91.1 Å
Shell Rg shell_rg	33.70 Å
Envelope Rg envelope_rg	26.76 Å
Shape Rg shape_rg	26.62 Å
Total Rg total_rg	27.32 Å
Total atoms total_atoms	4249
Residues n_residues	529
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	87.8 Å
Rg (real space) rg_real	27.58 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	6.4110e+07
I(0) uncertainty (real space) i0_real_error	9.3070e+05
Rg (reciprocal space) rg_reciprocal	27.58 Å
I(0) (reciprocal space) i0_reciprocal	64110000.0000
Solution quality estimate total_estimate	0.9038
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.8 Å
Skewness Skewness skewness	0.315
Kurtosis Kurtosis kurtosis	-0.513
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16360000.0000
Real-space data points n_real_points	59
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: 0.993; Smooth: 0.977

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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	Tyrosine-protein phosphatase non-receptor type 6
Molecular weight formula_weight	67640.0 kDa
EC 编号 ec_number	3.1.3.48
Mutation mutation	C453S
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	4266

MVRWFHRDLSGLDAETLLKGRGVHGSFLARPSRKNQGDFSLSVRVGDQVTHIRIQNSGDFYDLYGGEKFATLTELVEYYTQQQGVLQDRDGTIIHLKYPLNCSDPTSERWYHGHMSGGQAETLLQAKGEPWTFLVRESLSQPGDFVLSVLSDQPKAGPGSPLRVTHIKVMCEGGRYTVGGLETFDSLTDLVEHFKKTGIEEASGAFVYLRQPYYATRVNAADIENRVLELNKKQESEDTAKAGFWEEFESLQKQEVKNLHQRLEGQRPENKGKNRYKNILPFDHSRVILQGRDSNIPGSDYINANYIKNQLLGPDENAKTYIASQGCLEATVNDFWQMAWQENSRVIVMTTREVEKGRNKCVPYWPEVGMQRAYGPYSVTNCGEHDTTEYKLRTLQVSPLDNGDLIREIWHYQYLSWPDHGVPSEPGGVLSFLDQINQRQESLPHAGPIIVHSSAGIGRTGTIIVIDMLMENISTKGLDCDIDIQKTIQMVRAQRSGMVQTEAQYKFIYVAIAQFIETTKKKLEVLQSQKGQESEYGNITYPPAMKNAHAKASRTSSKHKEDVYENLHTKNKREEKVKKQRSADKEKSKGSLKRK

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 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	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	17

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3ps5a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.93 — SH2-like
Superfamily Superfamily superfamily	d.93.1 — SH2 domain
Family Family family	d.93.1.0 — automated matches

Domain ID domain_id	d3ps5a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.93 — SH2-like
Superfamily Superfamily superfamily	d.93.1 — SH2 domain
Family Family family	d.93.1.0 — automated matches

Domain ID domain_id	d3ps5a3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.45 — (Phosphotyrosine protein) phosphatases II
Superfamily Superfamily superfamily	c.45.1 — (Phosphotyrosine protein) phosphatases II
Family Family family	c.45.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	3ps5A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

Domain ID domain_id	3ps5A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

Domain ID domain_id	3ps5A03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily	10 — Protein tyrosine phosphatase superfamily

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8. Citations (1)

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Unit-cell length a length_a	231.919 Å
Unit-cell length b length_b	231.919 Å
Unit-cell length c length_c	78.852 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	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	115.960 Å
R factor r_factor	0.2272
R_work r_work	0.2248
R_free r_free	0.2758

fit	/app/data/saxs_computation/ps/3ps5/3ps5.fit
pddf	/app/data/pr_computation/ps/3ps5/3ps5.pr.out
profile	/app/data/saxs_computation/ps/3ps5/3ps5.dat

Crystal structure of the full-length Human Protein Tyrosine Phosphatase SHP-1

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

Tyrosine-protein phosphatase non-receptor type 6

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