SAXSdb — 9xrw

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

No usable UniProt protein identity is available for this entry.

七张关系表仍保留该条目的 assembly 与组成信息，但缺少统一蛋白身份时，不能可靠建立跨 PDB 的同蛋白Chain接。

Assembly Composition of the Current Entry

Assembly	Oligomeric State	实体与Construct证据	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Nucleic acid only No protein 蛋白 0 / DNA 2 / RNA 0 / 其他Polymer 0 PDB declaration: dimeric	Entity 1：;DNA (5'-D(CPCPGPCPGPCPGPTPGPCPCPGPCPGPAPA)-3') ; × 2 缺少 UniProt 身份时不显示参考序列区间	Not recorded	AG SILVER ION × 28 CL CHLORIDE ION × 2 SR STRONTIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；50 mM 3-(N-morpholino)propanesulfonic acid, 10 mM spermine, 10 mM Sr(NO3)2, 10% 2-methyl-2,4-pentanediol against a reservoir solution of 40% 2-methyl-2,4-pentanediol.	Resolution 1.90 Å R-free 0.156
2	Nucleic acid only No protein 蛋白 0 / DNA 2 / RNA 0 / 其他Polymer 0 PDB declaration: dimeric	Entity 1：;DNA (5'-D(CPCPGPCPGPCPGPTPGPCPCPGPCPGPAPA)-3') ; × 2 缺少 UniProt 身份时不显示参考序列区间	Not recorded	AG SILVER ION × 28 CL CHLORIDE ION × 2 SR STRONTIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；50 mM 3-(N-morpholino)propanesulfonic acid, 10 mM spermine, 10 mM Sr(NO3)2, 10% 2-methyl-2,4-pentanediol against a reservoir solution of 40% 2-methyl-2,4-pentanediol.	Resolution 1.90 Å R-free 0.156
3	Nucleic acid only No protein 蛋白 0 / DNA 2 / RNA 0 / 其他Polymer 0 PDB declaration: dimeric	Entity 1：;DNA (5'-D(CPCPGPCPGPCPGPTPGPCPCPGPCPGPAPA)-3') ; × 2 缺少 UniProt 身份时不显示参考序列区间	Not recorded	AG SILVER ION × 28 CL CHLORIDE ION × 2 SR STRONTIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；50 mM 3-(N-morpholino)propanesulfonic acid, 10 mM spermine, 10 mM Sr(NO3)2, 10% 2-methyl-2,4-pentanediol against a reservoir solution of 40% 2-methyl-2,4-pentanediol.	Resolution 1.90 Å R-free 0.156
4	Nucleic acid only No protein 蛋白 0 / DNA 2 / RNA 0 / 其他Polymer 0 PDB declaration: dimeric	Entity 1：;DNA (5'-D(CPCPGPCPGPCPGPTPGPCPCPGPCPGPAPA)-3') ; × 2 缺少 UniProt 身份时不显示参考序列区间	Not recorded	AG SILVER ION × 28 CL CHLORIDE ION × 2 SR STRONTIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；50 mM 3-(N-morpholino)propanesulfonic acid, 10 mM spermine, 10 mM Sr(NO3)2, 10% 2-methyl-2,4-pentanediol against a reservoir solution of 40% 2-methyl-2,4-pentanediol.	Resolution 1.90 Å R-free 0.156
5	Nucleic acid only No protein 蛋白 0 / DNA 2 / RNA 0 / 其他Polymer 0 PDB declaration: dimeric	Entity 1：;DNA (5'-D(CPCPGPCPGPCPGPTPGPCPCPGPCPGPAPA)-3') ; × 2 缺少 UniProt 身份时不显示参考序列区间	Not recorded	AG SILVER ION × 28 CL CHLORIDE ION × 2 SR STRONTIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；50 mM 3-(N-morpholino)propanesulfonic acid, 10 mM spermine, 10 mM Sr(NO3)2, 10% 2-methyl-2,4-pentanediol against a reservoir solution of 40% 2-methyl-2,4-pentanediol.	Resolution 1.90 Å R-free 0.156
6	Nucleic acid only No protein 蛋白 0 / DNA 2 / RNA 0 / 其他Polymer 0 PDB declaration: dimeric	Entity 1：;DNA (5'-D(CPCPGPCPGPCPGPTPGPCPCPGPCPGPAPA)-3') ; × 2 缺少 UniProt 身份时不显示参考序列区间	Not recorded	AG SILVER ION × 28 CL CHLORIDE ION × 2 SR STRONTIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；50 mM 3-(N-morpholino)propanesulfonic acid, 10 mM spermine, 10 mM Sr(NO3)2, 10% 2-methyl-2,4-pentanediol against a reservoir solution of 40% 2-methyl-2,4-pentanediol.	Resolution 1.90 Å R-free 0.156
7	Nucleic acid only No protein 蛋白 0 / DNA 2 / RNA 0 / 其他Polymer 0 PDB declaration: dimeric	Entity 1：;DNA (5'-D(CPCPGPCPGPCPGPTPGPCPCPGPCPGPAPA)-3') ; × 2 缺少 UniProt 身份时不显示参考序列区间	Not recorded	AG SILVER ION × 28 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；50 mM 3-(N-morpholino)propanesulfonic acid, 10 mM spermine, 10 mM Sr(NO3)2, 10% 2-methyl-2,4-pentanediol against a reservoir solution of 40% 2-methyl-2,4-pentanediol.	Resolution 1.90 Å R-free 0.156
8	Nucleic acid only No protein 蛋白 0 / DNA 2 / RNA 0 / 其他Polymer 0 PDB declaration: dimeric	Entity 1：;DNA (5'-D(CPCPGPCPGPCPGPTPGPCPCPGPCPGPAPA)-3') ; × 2 缺少 UniProt 身份时不显示参考序列区间	Not recorded	AG SILVER ION × 28 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；50 mM 3-(N-morpholino)propanesulfonic acid, 10 mM spermine, 10 mM Sr(NO3)2, 10% 2-methyl-2,4-pentanediol against a reservoir solution of 40% 2-methyl-2,4-pentanediol.	Resolution 1.90 Å R-free 0.156

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	9xrw
Deposition date deposition_date	2025-11-20
Structure title title	Probing Positions 3 and 8: Insights into a 960 nm emissive DNA-Stabilized Silver Nanocluster
Keywords keywords	DNA, silver, nanocluster, fluorescence; DNA
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	36.50 Å
Radius of gyration Rg (electron density) rg_electron	36.87 Å
Forward intensity I(0) i0	581855000.00
Molecular weight molecular_weight	103810.0 kDa
Excluded volume excluded_volume	84794 Å³
Envelope volume envelope_volume	128520 Å³
Hydration-shell volume shell_volume	31209 Å³
Envelope diameter envelope_diameter	124.1 Å
Shell Rg shell_rg	39.60 Å
Envelope Rg envelope_rg	36.28 Å
Shape Rg shape_rg	37.04 Å
Total Rg total_rg	36.74 Å
Total atoms total_atoms	5435
Residues n_residues	256
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	113.9 Å
Rg (real space) rg_real	36.76 Å
Rg uncertainty (real space) rg_real_error	1.14 Å
I(0) (real space) i0_real	5.8190e+08
I(0) uncertainty (real space) i0_real_error	9.9640e+06
Rg (reciprocal space) rg_reciprocal	36.60 Å
I(0) (reciprocal space) i0_reciprocal	581800000.0000
Solution quality estimate total_estimate	0.8136
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.1 Å
Skewness Skewness skewness	0.353
Kurtosis Kurtosis kurtosis	-0.582
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1150000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.894; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.892; Smooth: 0.010

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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	;DNA (5'-D(CPCPGPCPGPCPGPTPGPCPCPGPCPGPAPA)-3') ;
Molecular weight formula_weight	4885.2 kDa
Source method src_method	syn
Copy count entity_count	16

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A,B,D,E,G,H,J,K,M,N,P,Q,S,T,V,W
Atom count atom_count	5711

CCGCGCGTGCCGCGAA

Entity 2 Entity 2 non-polymer

Description description	SILVER ION
Molecular weight formula_weight	107.9 kDa
Source method src_method	syn
Copy count entity_count	224

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 4 Entity 4 non-polymer

Description description	STRONTIUM ION
Molecular weight formula_weight	87.6 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	276

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8. Citations (1)

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Unit-cell length a length_a	33.555 Å
Unit-cell length b length_b	108.107 Å
Unit-cell length c length_c	108.199 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	27.030 Å
R factor r_factor	0.1386
R_work r_work	0.1380
R_free r_free	0.1559

fit	/app/data/saxs_computation/xr/9xrw/9xrw.fit
pddf	/app/data/pr_computation/xr/9xrw/9xrw.pr.out
profile	/app/data/saxs_computation/xr/9xrw/9xrw.dat

Probing Positions 3 and 8: Insights into a 960 nm emissive DNA-Stabilized Silver Nanocluster

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

Assembly Composition of the Current Entry

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