SAXSdb — 4rcb

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

RNA-binding protein Hfq

OrganismNot specified

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 5–71	Fragment：UNP RESIDUES 5-71	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；0.5M Lithium chloride, 1.6M Ammonium sulfate , VAPOR DIFFUSION, SITTING DROP	Resolution 1.63 Å R-free 0.248

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 4RCB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HK9 Crystal structure of the Hfq protein from Escherichia coli Deposited 2003-03-06	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–72（72 aa） Fragment：RESIDUES 1-72 Chain B 1–72（72 aa） Fragment：RESIDUES 1-72 Chain C 1–72（72 aa） Fragment：RESIDUES 1-72 Chain D 1–72（72 aa） Fragment：RESIDUES 1-72 Chain E 1–72（72 aa） Fragment：RESIDUES 1-72 Chain F 1–72（72 aa） Fragment：RESIDUES 1-72	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；CRYSTALS WERE OBTAINED BY VAPOR DIFFUSION IN 2UL SITTING DROPS. THE RESERVOIR CONTAINED 25% PEG 4000, 0.2 M NH4-ACETATE AND 0.2 M NA-ACETATE PH 4.6. CRYSTALLIZATION WERE CARRIED OUT AT 20C.	Resolution 2.15 Å R-free 0.262
2Y90 Crystal structure of Hfq riboregulator from E. coli (P6 space group) Deposited 2011-02-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–102（102 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；CRYSTALS WERE OBTAINED BY VAPOR DIFFUSION IN 2UL HANGING DROPS AT 20C. THE RESERVOIR CONTAINED 1.6 M AMMONIUM SULFATE, 0.1 M TRIS-HCL PH 8.0.	Resolution 2.25 Å R-free 0.226
2YHT Crystal structure of Hfq riboregulator from E. coli (P1 space group) Deposited 2011-05-06	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–72（72 aa） Fragment：SM-LIKE FOLD, RESIDUES 1-72 Chain B 1–72（72 aa） Fragment：SM-LIKE FOLD, RESIDUES 1-72 Chain C 1–72（72 aa） Fragment：SM-LIKE FOLD, RESIDUES 1-72 Chain D 1–72（72 aa） Fragment：SM-LIKE FOLD, RESIDUES 1-72 Chain E 1–72（72 aa） Fragment：SM-LIKE FOLD, RESIDUES 1-72 Chain F 1–72（72 aa） Fragment：SM-LIKE FOLD, RESIDUES 1-72	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；293 K；CRYSTALS WERE OBTAINED BY VAPOR DIFFUSION IN 2UL SITTING DROPS. THE RESERVOIR CONTAINED 30% PEG 3350, 0.1 M NA-CITRATE PH 5.4. CRYSTALLIZATIONS WERE CARRIED OUT AT 20 DEGREES CELSIUS.	Resolution 2.90 Å R-free 0.229
2YHT Crystal structure of Hfq riboregulator from E. coli (P1 space group) Deposited 2011-05-06	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 1–72（72 aa） Fragment：SM-LIKE FOLD, RESIDUES 1-72 Chain H 1–72（72 aa） Fragment：SM-LIKE FOLD, RESIDUES 1-72 Chain I 1–72（72 aa） Fragment：SM-LIKE FOLD, RESIDUES 1-72 Chain J 1–72（72 aa） Fragment：SM-LIKE FOLD, RESIDUES 1-72 Chain K 1–72（72 aa） Fragment：SM-LIKE FOLD, RESIDUES 1-72 Chain L 1–72（72 aa） Fragment：SM-LIKE FOLD, RESIDUES 1-72	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；293 K；CRYSTALS WERE OBTAINED BY VAPOR DIFFUSION IN 2UL SITTING DROPS. THE RESERVOIR CONTAINED 30% PEG 3350, 0.1 M NA-CITRATE PH 5.4. CRYSTALLIZATIONS WERE CARRIED OUT AT 20 DEGREES CELSIUS.	Resolution 2.90 Å R-free 0.229
3GIB Crystal Structure of the Complex of the E. coli Hfq with Poly(A) Deposited 2009-03-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 6 PDB declaration: octameric	Chain A 2–69（68 aa） Fragment：N-terminal fragment (2-69) Chain B 2–69（68 aa） Fragment：N-terminal fragment (2-69) Chain C 2–69（68 aa） Fragment：N-terminal fragment (2-69)	Not recorded	NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 9.5；298 K；40% MPD, 0.1 M CHES 9.5, hanging drop, temperature 298K	Resolution 2.40 Å R-free 0.259
3QHS Crystal structure of full-length Hfq from Escherichia coli Deposited 2011-01-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–102（102 aa） Chain B 1–102（102 aa） Chain C 1–102（102 aa） Chain D 1–102（102 aa） Chain E 1–102（102 aa） Chain F 1–102（102 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；30% v/v PEG 550 MME, 0.05M calcium chloride dihydrate, 0.1M BIS-TRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.85 Å R-free 0.250
3QHS Crystal structure of full-length Hfq from Escherichia coli Deposited 2011-01-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 1–102（102 aa） Chain H 1–102（102 aa） Chain I 1–102（102 aa） Chain J 1–102（102 aa） Chain K 1–102（102 aa） Chain L 1–102（102 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；30% v/v PEG 550 MME, 0.05M calcium chloride dihydrate, 0.1M BIS-TRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.85 Å R-free 0.250
3QO3 Crystal structure of Escherichia coli Hfq, in complex with ATP Deposited 2011-02-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–65（65 aa） Fragment：N-terminal (L)Sm core-domain, UNP residues 1-65 Chain B 1–65（65 aa） Fragment：N-terminal (L)Sm core-domain, UNP residues 1-65 Chain C 1–65（65 aa） Fragment：N-terminal (L)Sm core-domain, UNP residues 1-65 Chain D 1–65（65 aa） Fragment：N-terminal (L)Sm core-domain, UNP residues 1-65 Chain E 1–65（65 aa） Fragment：N-terminal (L)Sm core-domain, UNP residues 1-65 Chain F 1–65（65 aa） Fragment：N-terminal (L)Sm core-domain, UNP residues 1-65	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；0.1M Hepes, 10% (W/V) PEG 8000, 8% (V/V) Ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.15 Å R-free 0.257
3VU3 Crystal structure of the Hfq and catalase HPII complex Deposited 2012-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric	Chain C 1–102（102 aa） Chain D 1–102（102 aa） Chain E 1–102（102 aa） Chain F 1–102（102 aa） Chain G 1–102（102 aa） Chain H 1–102（102 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；0.1M Tris-HCl, 0.18M NaCl, 10% PEG4000, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.85 Å R-free 0.246
4JRI Crystal Structure of Escherichia coli Hfq Proximal Edge Mutant Deposited 2013-03-21	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–69（68 aa） Fragment：UNP residues 2-69 Chain B 2–69（68 aa） Fragment：UNP residues 2-69	Mutation：F39W Mutation：F39W	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.83 Å R-free 0.257
4JRI Crystal Structure of Escherichia coli Hfq Proximal Edge Mutant Deposited 2013-03-21	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain C 2–69（68 aa） Fragment：UNP residues 2-69 Chain D 2–69（68 aa） Fragment：UNP residues 2-69	Mutation：F39W Mutation：F39W	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.83 Å R-free 0.257
4JRK Crystal Structure of Escherichia coli Hfq Surface Mutant Deposited 2013-03-21	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–69（68 aa） Fragment：UNP residues 2-69 Chain B 2–69（68 aa） Fragment：UNP residues 2-69 Chain C 2–69（68 aa） Fragment：UNP residues 2-69	Mutation：F11W Mutation：F11W Mutation：F11W	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.89 Å R-free 0.216
4JUV Crystal Structure of Escherichia coli Hfq Distal Face 1 Mutant Deposited 2013-03-25	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–69（68 aa） Chain B 2–69（68 aa） Chain C 2–69（68 aa） Chain D 2–69（68 aa） Chain E 2–69（68 aa） Chain F 2–69（68 aa）	Mutation：Y25W Mutation：Y25W Mutation：Y25W Mutation：Y25W Mutation：Y25W Mutation：Y25W	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.19 Å
4RCC Crystal structure of E Coli Hfq Deposited 2014-09-15	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 5–71（67 aa） Fragment：UNP RESIDUES 5-71	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；0.1M TRIS.HCl pH 8.5, 1.5M Ammonium sulfate, 15 %(w/v) Glycerol, VAPOR DIFFUSION, SITTING DROP	Resolution 1.98 Å R-free 0.213
4V2S Crystal structure of Hfq in complex with the sRNA RydC Deposited 2014-10-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 6 PDB declaration: heptameric	Chain A 1–102（102 aa） Chain B 1–102（102 aa） Chain C 1–102（102 aa） Chain D 1–102（102 aa） Chain E 1–102（102 aa） Chain F 1–102（102 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.2 M TRI-SODIUM CITRATE, 0.1 M SODIUM CACODYLATE (PH 6.5), 15% ISOPROPANOL	Resolution 3.48 Å R-free 0.282
9GU5 Crystal Structure of Hfq V22A Deposited 2024-09-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 6 PDB declaration: heptameric	Chain A 1–102（102 aa） Chain B 1–102（102 aa） Chain C 1–102（102 aa） Chain D 1–102（102 aa） Chain E 1–102（102 aa） Chain F 1–102（102 aa）	Mutation：V22A Mutation：V22A Mutation：V22A Mutation：V22A Mutation：V22A Mutation：V22A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；22.5 %v/v PEGSB, 0.2 M LiSO4, 0.05 M Zn Acet, 0.1 M BIS-TRIS	Resolution 2.90 Å R-free 0.387
9GU5 Crystal Structure of Hfq V22A Deposited 2024-09-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 1–102（102 aa） Chain H 1–102（102 aa） Chain I 1–102（102 aa） Chain J 1–102（102 aa） Chain K 1–102（102 aa） Chain L 1–102（102 aa）	Mutation：V22A Mutation：V22A Mutation：V22A Mutation：V22A Mutation：V22A Mutation：V22A	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；22.5 %v/v PEGSB, 0.2 M LiSO4, 0.05 M Zn Acet, 0.1 M BIS-TRIS	Resolution 2.90 Å R-free 0.387
9H45 Crystal Structure of Hfq V22A Deposited 2024-10-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 6 PDB declaration: heptameric	Chain A 1–102（102 aa） Chain B 1–102（102 aa） Chain C 1–102（102 aa） Chain D 1–102（102 aa） Chain E 1–102（102 aa） Chain F 1–102（102 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；15 %v/v PEGSH 0.15 M NH4 Acet 0.1 M Na3 Cit	Resolution 2.08 Å R-free 0.323

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

View Construct and Data Evidence

UniProt name	HFQ_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–67； UniProt 5–71

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	4rcb
Deposition date deposition_date	2014-09-15
Structure title title	Crystal structure of E Coli Hfq
Keywords keywords	RNA binding protein; RNA 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	12.97 Å
Radius of gyration Rg (electron density) rg_electron	11.45 Å
Forward intensity I(0) i0	1246220.00
Molecular weight molecular_weight	7630.0 kDa
Excluded volume excluded_volume	9704 Å³
Envelope volume envelope_volume	10914 Å³
Hydration-shell volume shell_volume	8413 Å³
Envelope diameter envelope_diameter	39.2 Å
Shell Rg shell_rg	16.68 Å
Envelope Rg envelope_rg	11.77 Å
Shape Rg shape_rg	11.44 Å
Total Rg total_rg	12.93 Å
Total atoms total_atoms	539
Residues n_residues	67
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	42.0 Å
Rg (real space) rg_real	12.87 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	1.2460e+06
I(0) uncertainty (real space) i0_real_error	1.3520e+04
Rg (reciprocal space) rg_reciprocal	12.88 Å
I(0) (reciprocal space) i0_reciprocal	1246000.0000
Solution quality estimate total_estimate	0.8837
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.6 Å
Skewness Skewness skewness	0.069
Kurtosis Kurtosis kurtosis	-0.354
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	171000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.982

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4rcba_
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.2 — Pleiotropic translational regulator Hfq

CATH v4.4 (1 domains)

Domain ID domain_id	4rcbA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

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8. Citations (1)

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Unit-cell length a length_a	61.270 Å
Unit-cell length b length_b	61.270 Å
Unit-cell length c length_c	28.160 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	6

Space group space_group	P 6
Space-group number int_tables_number	168
Crystal system crystal_system	—

Resolution resolution	1.630 Å
Low-resolution limit resolution_low	26.531 Å
R factor r_factor	0.2176
R_work r_work	0.2158
R_free r_free	0.2480

Description description	RNA-binding protein Hfq
Molecular weight formula_weight	7653.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	575

Crystal structure of E Coli Hfq

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

RNA-binding protein Hfq

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	36

fit	/app/data/saxs_computation/rc/4rcb/4rcb.fit
pddf	/app/data/pr_computation/rc/4rcb/4rcb.pr.out
profile	/app/data/saxs_computation/rc/4rcb/4rcb.dat