SAXSdb — 4wh9

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

M-phase inducer phosphatase 2

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 386–565	Fragment：catalytic domain (UNP residues 386-565) Mutation：C473S	3M8 2-[(2-cyano-3-fluoro-5-hydroxyphenyl)sulfanyl]ethanesulfonic acid × 1 SO4 SULFATE ION × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；(NH4)2SO4, Tris, TCEP	Resolution 1.50 Å R-free 0.152

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 4WH9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CWR HUMAN CDC25B CATALYTIC DOMAIN WITHOUT ION IN CATALYTIC SITE Deposited 1999-08-26	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 356–566（211 aa） Fragment：CATALYTIC DOMAIN	Not recorded	SO4 SULFATE ION × 1 BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；4 MICROLITERS PROTEIN (10 MG/ ML IN 50 MM TRISHCL, 1% BME AT PH 9.0) MIXED WITH 4 MICROLITERS WELL BUFFER (1.8 (NH4)2SO4, 0.5 M NACL, 0.1 M TRISHCL, 0.25 BME) AT 4 DEG. C	Resolution 2.10 Å
1CWS HUMAN CDC25B CATALYTIC DOMAIN WITH TUNGSTATE Deposited 1999-08-26	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 329–539（211 aa） Fragment：CATALYTIC DOMAIN	Not recorded	WO4 TUNGSTATE(VI)ION × 1 SO4 SULFATE ION × 1 CL CHLORIDE ION × 1 BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；4 MICROLITERS PROTEIN (10 MG/ ML IN 50 MM TRISHCL, WO4=,1% BME AT PH 9.0) MIXED WITH 4 MICROLITERS WELL BUFFER (1.8 (NH4)2SO4, 0.5 M NACL, 0.1 M TRISHCL, 0.25 BME) AT 4 DEG. C	Resolution 2.00 Å
1CWT HUMAN CDC25B CATALYTIC DOMAIN WITH METHYL MERCURY Deposited 1999-08-26	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 347–524（178 aa） Fragment：CATALYTIC DOMAIN	Not recorded	SO4 SULFATE ION × 2 CL CHLORIDE ION × 1 MMC METHYL MERCURY ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；4 MICROLITERS PROTEIN (10 MG/ ML IN 50 MM TRISHCL, CH(3)HGCL,1% BME AT PH 9.0) MIXED WITH 4 MICROLITERS WELL BUFFER (1.8 (NH4)2SO4, 0.5 M NACL, 0.1 M TRISHCL, 0.25 BME) AT 4 DEG. C	Resolution 2.30 Å
1QB0 HUMAN CDC25B CATALYTIC DOMAIN Deposited 1999-04-29	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 356–566（211 aa） Fragment：CATALYTIC DOMAIN	Not recorded	SO4 SULFATE ION × 2 CL CHLORIDE ION × 1 BME BETA-MERCAPTOETHANOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；277 K；4 MICROLITERS PROTEIN (10 MG/ML IN 50 MM TRISHCL, 1% BME AT PH 9.0) MIXED WITH 4 MICROLITERS WELL BUFFER (1.8 (NH4)2SO4, 0.5 M NACL, 0.1 M TRISHCL, 0.25 BME) AT 4 DEG. C, VAPOR DIFFUSION, SITTING DROP, temperature 4.0K	Resolution 1.91 Å
1YM9 Crystal structure of the CDC25B phosphatase catalytic domain with the active site cysteine in the sulfinic form Deposited 2005-01-20	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 391–564（174 aa） Fragment：catalytic domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.25；DTT, Tris, Ammonium Sulfate, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 100.0K	Resolution 2.00 Å R-free 0.237
1YMD Crystal Structure of the CDC25B phosphatase catalytic domain with the active site cysteine in the sulfonic form Deposited 2005-01-20	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 391–564（174 aa） Fragment：catalytic domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.25；DTT, Tris, Ammonium Sulfate, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 100.0K	Resolution 1.70 Å R-free 0.209
1YMK Crystal Structure of the CDC25B phosphatase catalytic domain in the apo form Deposited 2005-01-21	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 391–564（174 aa） Fragment：catalytic domain	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.25；DTT,Tris, Ammonium Sulfate, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 100.0K	Resolution 1.70 Å R-free 0.196
1YML Crystal Structure of the CDC25B phosphatase catalytic domain with the active site cysteine in the sulfenic form Deposited 2005-01-21	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 391–564（174 aa） Fragment：catalytic domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.25；DTT,Tris, Ammonium Sulfate, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 100.0K	Resolution 1.70 Å R-free 0.208
1YS0 Crystal Structure of the CDC25B phosphatase catalytic domain with the active site cysteine in the disulfide form Deposited 2005-02-05	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 391–564（174 aa） Fragment：catalytic domain	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.25；DTT, Tris, Ammonium Sulfate, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 100.0K	Resolution 2.00 Å R-free 0.244
2A2K Crystal Structure of an active site mutant, C473S, of Cdc25B Phosphatase Catalytic Domain Deposited 2005-06-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 377–550（174 aa） Fragment：Catalytic Domain	Mutation：C473S	CL CHLORIDE ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；DTT, Ammonium Sulfate, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.52 Å R-free 0.191
2IFD Crystal structure of a remote binding site mutant, R492L, of CDC25B Phosphatase catalytic domain Deposited 2006-09-20	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 391–564（174 aa） Fragment：CATALYTIC DOMAIN, residues 391-564	Mutation：R492L	SO4 SULFATE ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；DTT, AMMONIUM SULFATE, TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.212
2IFV Crystal structure of an active site mutant, C473D, of CDC25B phosphatase catalytic domain Deposited 2006-09-21	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 391–564（174 aa） Fragment：Catalytic domain, residues 391-564	Mutation：C473D	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；DTT, AMMONIUM SULFATE, TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.60 Å R-free 0.192
2UZQ Protein Phosphatase, New Crystal Form Deposited 2007-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 377–566（190 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 377-566 Chain B 377–566（190 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 377-566	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PEG 8000, HEPES PH 7.0, GUANIDINIUM CHLORIDE	Resolution 2.38 Å R-free 0.249
2UZQ Protein Phosphatase, New Crystal Form Deposited 2007-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 377–566（190 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 377-566 Chain D 377–566（190 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 377-566	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PEG 8000, HEPES PH 7.0, GUANIDINIUM CHLORIDE	Resolution 2.38 Å R-free 0.249
2UZQ Protein Phosphatase, New Crystal Form Deposited 2007-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 377–566（190 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 377-566 Chain F 377–566（190 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 377-566	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PEG 8000, HEPES PH 7.0, GUANIDINIUM CHLORIDE	Resolution 2.38 Å R-free 0.249
4WH7 Structure of the CDC25B Phosphatase Catalytic Domain with Bound Ligand Deposited 2014-09-20	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 386–565（180 aa） Fragment：catalytic domain (UNP residues 386-565)	Mutation：C473S	SO4 SULFATE ION × 6 8H8 2-fluoro-4-hydroxybenzonitrile × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；(NH4)2SO4, Tris, TCEP	Resolution 1.62 Å R-free 0.198
9T09 X-ray structure of the catalytic domain of CDC25B C473S at 1.34 angstrom resolution Deposited 2025-10-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 391–564（174 aa）	Mutation：C473S	SO4 SULFATE ION × 4 CL CHLORIDE ION × 1 ZN ZINC ION × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；2.0 M ammonium sulphate, 0.5 M NaCl, 0.1 M Tris-HCl pH 7.5, and 0.5 mM TCEP	Resolution 1.34 Å R-free 0.175
9T0A X-ray structure of the complex between the catalytic domain of CDC25B C473S and 3-O-methylfluorescein phosphate (3-OMFP) Deposited 2025-10-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 391–564（174 aa）	Mutation：C473S	A1JSQ [(1~{R})-6'-methoxy-3-oxidanylidene-spiro[2-benzofuran-1,9'-xanthene]-3'-yl] dihydrogen phosphate × 1 A1JSP [(1~{S})-6'-methoxy-3-oxidanylidene-spiro[2-benzofuran-1,9'-xanthene]-3'-yl] dihydrogen phosphate × 1 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；3.8 M NaCl, 0.1 M HEPES pH 7.5, and 1.2% v/v 2-propanol	Resolution 2.04 Å R-free 0.214

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

View Construct and Data Evidence

UniProt name	MPIP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–183； UniProt 386–565

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	4wh9
Deposition date deposition_date	2014-09-20
Structure title title	Structure of the CDC25B Phosphatase Catalytic Domain with Bound Inhibitor
Keywords keywords	Phosphatase, Inhibitor, Fragment, HYDROLASE-HYDROLASE Inhibitor complex; HYDROLASE/HYDROLASE Inhibitor
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	17.46 Å
Radius of gyration Rg (electron density) rg_electron	16.27 Å
Forward intensity I(0) i0	8828050.00
Molecular weight molecular_weight	21607.0 kDa
Excluded volume excluded_volume	26884 Å³
Envelope volume envelope_volume	30571 Å³
Hydration-shell volume shell_volume	15729 Å³
Envelope diameter envelope_diameter	56.8 Å
Shell Rg shell_rg	22.55 Å
Envelope Rg envelope_rg	16.70 Å
Shape Rg shape_rg	16.28 Å
Total Rg total_rg	17.30 Å
Total atoms total_atoms	1515
Residues n_residues	177
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	57.9 Å
Rg (real space) rg_real	17.38 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	8.8280e+06
I(0) uncertainty (real space) i0_real_error	1.1290e+05
Rg (reciprocal space) rg_reciprocal	17.39 Å
I(0) (reciprocal space) i0_reciprocal	8828000.0000
Solution quality estimate total_estimate	0.7992
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.1 Å
Skewness Skewness skewness	0.229
Kurtosis Kurtosis kurtosis	-0.286
Angular range angular_range	— – 0.4550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2419000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.802; Stabil: 0.994; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	M-phase inducer phosphatase 2
Molecular weight formula_weight	21449.4 kDa
EC 编号 ec_number	3.1.3.48
Mutation mutation	C473S
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	1873

GSSDSDHRELIGDYSKAFLLQTVDGKHQDLKYISPETMVALLTGKFSNIVDKFVIVDCRYPYEYEGGHIKTAVNLPLERDAESFLLKSPIAPCSLDKRVILIFHSEFSSERGPRMCRFIRERDRAVNDYPSLYYPEMYILKGGYKEFFPQHPNFCEPQDYRPMNHEAFKDELKTFRLKTRSWA

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	2-[(2-cyano-3-fluoro-5-hydroxyphenyl)sulfanyl]ethanesulfonic acid
Molecular weight formula_weight	277.3 kDa
Source method src_method	syn
Copy count entity_count	1

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	4

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	296

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4wh9a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.46 — Rhodanese/Cell cycle control phosphatase
Superfamily Superfamily superfamily	c.46.1 — Rhodanese/Cell cycle control phosphatase
Family Family family	c.46.1.1 — Cell cycle control phosphatase, catalytic domain

CATH v4.4 (1 domains)

Domain ID domain_id	4wh9A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	250 — Oxidized Rhodanese; domain 1
Homologous superfamily homologous superfamily	10 — Rhodanese-like domain

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8. Citations (1)

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Unit-cell length a length_a	51.660 Å
Unit-cell length b length_b	71.470 Å
Unit-cell length c length_c	73.940 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	51.390 Å
R factor r_factor	0.1273
R_work r_work	0.1260
R_free r_free	0.1520

fit	/app/data/saxs_computation/wh/4wh9/4wh9.fit
pddf	/app/data/pr_computation/wh/4wh9/4wh9.pr.out
profile	/app/data/saxs_computation/wh/4wh9/4wh9.dat

Structure of the CDC25B Phosphatase Catalytic Domain with Bound Inhibitor

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

M-phase inducer phosphatase 2

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