SAXSdb — 6sdm

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

NADP-dependent isopropanol dehydrogenase

Thermoanaerobacter brockii

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–352 Chain B； UniProt 1–352 Chain C； UniProt 1–352 Chain D； UniProt 1–352	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5.5；298 K；20% w/v PEG 3K, sodium citrate pH 5.5	Resolution 2.85 Å R-free 0.238

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 6SDM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BXZ CRYSTAL STRUCTURE OF A THERMOPHILIC ALCOHOL DEHYDROGENASE SUBSTRATE COMPLEX FROM THERMOANAEROBACTER BROCKII Deposited 1998-10-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–352（352 aa） Fragment：NUCLEOTIDE-BINDING DOMAIN, CATALYTIC DOMAIN Chain B 1–352（352 aa） Fragment：NUCLEOTIDE-BINDING DOMAIN, CATALYTIC DOMAIN Chain C 1–352（352 aa） Fragment：NUCLEOTIDE-BINDING DOMAIN, CATALYTIC DOMAIN Chain D 1–352（352 aa） Fragment：NUCLEOTIDE-BINDING DOMAIN, CATALYTIC DOMAIN	Not recorded	ZN ZINC ION × 4 CL CHLORIDE ION × 4 MG MAGNESIUM ION × 4 SBT 2-BUTANOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；pH 5.8	Resolution 2.99 Å R-free 0.264
1YKF NADP-DEPENDENT ALCOHOL DEHYDROGENASE FROM THERMOANAEROBIUM BROCKII Deposited 1996-03-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–352（352 aa） Chain B 1–352（352 aa） Chain C 1–352（352 aa） Chain D 1–352（352 aa）	Not recorded	ZN ZINC ION × 4 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.2；pH 8.2	Resolution 2.50 Å R-free 0.267
2NVB Contribution of Pro275 to the Thermostability of the Alcohol Dehydrogenases (ADHs) Deposited 2006-11-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–352（352 aa） Chain B 1–352（352 aa） Chain C 1–352（352 aa） Chain D 1–352（352 aa）	Mutation：P275D Mutation：P275D Mutation：P275D Mutation：P275D	ZN ZINC ION × 4 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；298 K；16%(w/v) PEG 4000, 50mM NaCl, 50mM Tris-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.3	Resolution 2.80 Å R-free 0.278
2NVB Contribution of Pro275 to the Thermostability of the Alcohol Dehydrogenases (ADHs) Deposited 2006-11-12	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 A 1–352（352 aa） Chain B 1–352（352 aa）	Mutation：P275D Mutation：P275D	ZN ZINC ION × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；298 K；16%(w/v) PEG 4000, 50mM NaCl, 50mM Tris-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.3	Resolution 2.80 Å R-free 0.278
2NVB Contribution of Pro275 to the Thermostability of the Alcohol Dehydrogenases (ADHs) Deposited 2006-11-12	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 C 1–352（352 aa） Chain D 1–352（352 aa）	Mutation：P275D Mutation：P275D	ZN ZINC ION × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；298 K；16%(w/v) PEG 4000, 50mM NaCl, 50mM Tris-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.3	Resolution 2.80 Å R-free 0.278
3FPC Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-294 of T. brockii ADH by E. histolytica ADH Deposited 2009-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–152（152 aa） Chain A 295–352（58 aa） Chain B 1–152（152 aa） Chain B 295–352（58 aa） Chain C 1–152（152 aa） Chain C 295–352（58 aa） Chain D 1–152（152 aa） Chain D 295–352（58 aa）	Not recorded	ZN ZINC ION × 4 CAC CACODYLATE ION × 4 OXY OXYGEN MOLECULE × 1 EDO 1,2-ETHANEDIOL × 14 NO3 NITRATE ION × 2 IMD IMIDAZOLE × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；8mg/mL protein [25mM Tris-HCl, 50mM NaCl, 0.1mM DTT, 50mM ZnCl2 (pH=7.5)] was mixed with 0.001 ml of reservoir solution [16% (w/v) PEG 8000, 200mM magnesium acetate tetrahydrate, 100mM Cacodylate buffer (pH 6.5)], vapor diffusion, hanging drop, temperature 298K	Resolution 1.40 Å R-free 0.155
3FPL Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-295 of C. beijerinckii ADH by T. brockii ADH Deposited 2009-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 153–295（143 aa）	Not recorded	ZN ZINC ION × 4 CL CHLORIDE ION × 8 EDO 1,2-ETHANEDIOL × 4 CAC CACODYLATE ION × 4 PGE TRIETHYLENE GLYCOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；298 K；Single crystals of apo-22(CTC) were obtained by the microbatch method under oil at 18 C, using the IMPAX 1-5 robot. The apo-22(CTC) (10mg/mL) was crystallized in a mixture containing 100mM ammonium acetate, 15% (w/v) PEG 4000, 25mM NaCl, 50mM DTT, 25mM ZnCl2 and 50mM tri-citrate dihydrate (pH sodium 5.6), Microbatch, temperature 298K	Resolution 1.90 Å R-free 0.172
3FSR Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-295 of T. brockii ADH by C. beijerinckii ADH Deposited 2009-01-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–152（152 aa） Chain A 296–352（57 aa） Chain B 1–152（152 aa） Chain B 296–352（57 aa） Chain C 1–152（152 aa） Chain C 296–352（57 aa） Chain D 1–152（152 aa） Chain D 296–352（57 aa）	Not recorded	ZN ZINC ION × 6 EDO 1,2-ETHANEDIOL × 5 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；8mg/mL protein [25mM Tris-HCl, 50mM NaCl, 0.1mM DTT, 50mM ZnCl2 (pH=7.5)] was mixed with 0.001ml of reservoir solution [16% (w/v) PEG 8000, 200mM magnesium acetate tetrahydrate, 100mM Cacodylate buffer (pH 6.5)], vapor diffusion, hanging drop, temperature 298K	Resolution 2.20 Å R-free 0.220
3FTN Q165E/S254K Double Mutant Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-295 of T. brockii ADH by C. beijerinckii ADH Deposited 2009-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–152（152 aa） Chain A 296–352（57 aa） Chain B 1–152（152 aa） Chain B 296–352（57 aa） Chain C 1–152（152 aa） Chain C 296–352（57 aa） Chain D 1–152（152 aa） Chain D 296–352（57 aa）	Mutation：Q165E, S254K Mutation：Q165E, S254K Mutation：Q165E, S254K Mutation：Q165E, S254K Mutation：Q165E, S254K Mutation：Q165E, S254K Mutation：Q165E, S254K Mutation：Q165E, S254K	ZN ZINC ION × 4 ACT ACETATE ION × 4 EDO 1,2-ETHANEDIOL × 11 CL CHLORIDE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；8 mg/mL protein, 25 mM Tris-HCl, 50 mM NaCl, 0.1 mM DTT, 50 mM ZnCl2 (pH=7.5)] was mixed with 1 microliter of reservoir solution [16% (w/v) PEG8K, 200 mM magnesium acetate tetrahydrate, 100 mM Cacodylate buffer (pH 6.5), vapor diffusion, hanging drop, temperature 298K	Resolution 2.19 Å R-free 0.228
7F3P Crystal structure of a nadp-dependent alcohol dehydrogenase mutant in apo form Deposited 2021-06-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–352（352 aa） Chain B 1–352（352 aa） Chain C 1–352（352 aa） Chain D 1–352（352 aa）	Mutation：P84S, I86L Mutation：P84S, I86L Mutation：P84S, I86L Mutation：P84S, I86L	ZN ZINC ION × 4 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；PEG3350, NH4, citrate	Resolution 2.60 Å R-free 0.237
7UTC Crystal structure of secondary alcohol dehydrogenases from the Thermoanaerobacter ethanolicus with NADP and transition-state analogue inhibitor DMSO Deposited 2022-04-26	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–352（352 aa） Chain B 1–352（352 aa） Chain C 1–352（352 aa） Chain D 1–352（352 aa）	Mutation：C295A Mutation：C295A Mutation：C295A Mutation：C295A	ZN ZINC ION × 4 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 DMS DIMETHYL SULFOXIDE × 35	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.6 M KCl, 12% PEG 3350, 50 mM HEPES-K buffer, pH 7.5	Resolution 1.85 Å R-free 0.227
7UUT Ternary complex crystal structure of secondary alcohol dehydrogenases from the Thermoanaerobacter ethanolicus mutants C295A and I86A provides better understanding of catalytic mechanism Deposited 2022-04-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–352（352 aa） Chain B 1–352（352 aa） Chain C 1–352（352 aa） Chain D 1–352（352 aa）	Mutation：I86A Mutation：I86A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：I86A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：I86A Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 4 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 2RP (2R)-pentan-2-ol × 4 K POTASSIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；0.6 M KCl, 12% PEG 3350, 50 mM HEPES buffer pH 7.5	Resolution 1.89 Å R-free 0.231
7UX4 Crystallographic snapshots of ternary complexes of thermophilic secondary alcohol dehydrogenase from Thermoanaerobacter pseudoethanolicus reveal the dynamics of ligand exchange and the proton relay network. Deposited 2022-05-04	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–352（352 aa） Chain B 1–352（352 aa） Chain C 1–352（352 aa） Chain D 1–352（352 aa）	Mutation：I86A Mutation：I86A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：I86A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：I86A Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 4 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 K POTASSIUM ION × 8 NWO (1S,3S)-3-methylcyclohexan-1-ol × 3 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.6 M KCl,12% PEG 3350, 50 mM HEPES-K buffer, pH 7.5	Resolution 2.23 Å R-free 0.204
7XL5 Crystal structure of the H42T/A85G/I86A mutant of a nadp-dependent alcohol dehydrogenase Deposited 2022-04-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–352（351 aa） Chain B 2–352（351 aa） Chain C 2–352（351 aa） Chain D 2–352（351 aa）	Mutation：H42T, A85G, I86A Mutation：H42T, A85G, I86A Mutation：H42T, A85G, I86A Mutation：H42T, A85G, I86A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M Magnesium acetate tetrahydrate, 15% (w/v) PEG 3350	Resolution 2.60 Å R-free 0.225
7XY9 Cryo-EM structure of secondary alcohol dehydrogenases TbSADH after carrier-free immobilization based on weak intermolecular interactions Deposited 2022-06-01	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–352（351 aa） Chain B 2–352（351 aa） Chain C 2–352（351 aa） Chain D 2–352（351 aa）	Mutation：I86N Mutation：I86N Mutation：I86N Mutation：I86N	ZN ZINC ION × 4 MG MAGNESIUM ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.12 Å

13 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ADH_THEBR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–354； UniProt 1–352 Author chain B； PDBConstruct 3–354； UniProt 1–352 Author chain C； PDBConstruct 3–354； UniProt 1–352 Author chain D； PDBConstruct 3–354； UniProt 1–352

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	6sdm
Deposition date deposition_date	2019-07-28
Structure title title	NADH-dependent variant of TBADH
Keywords keywords	oxidoreductase, cofactor; OXIDOREDUCTASE
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	32.98 Å
Radius of gyration Rg (electron density) rg_electron	32.36 Å
Forward intensity I(0) i0	335818000.00
Molecular weight molecular_weight	151570.0 kDa
Excluded volume excluded_volume	191520 Å³
Envelope volume envelope_volume	228990 Å³
Hydration-shell volume shell_volume	56304 Å³
Envelope diameter envelope_diameter	105.4 Å
Shell Rg shell_rg	41.20 Å
Envelope Rg envelope_rg	32.30 Å
Shape Rg shape_rg	32.36 Å
Total Rg total_rg	32.99 Å
Total atoms total_atoms	10622
Residues n_residues	1415
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	100.1 Å
Rg (real space) rg_real	32.72 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	3.3580e+08
I(0) uncertainty (real space) i0_real_error	4.5300e+06
Rg (reciprocal space) rg_reciprocal	32.83 Å
I(0) (reciprocal space) i0_reciprocal	335900000.0000
Solution quality estimate total_estimate	0.9023
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	43.8 Å
Skewness Skewness skewness	0.099
Kurtosis Kurtosis kurtosis	-0.538
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	157100000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.937

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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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8. Citations (1)

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Unit-cell length a length_a	79.123 Å
Unit-cell length b length_b	123.946 Å
Unit-cell length c length_c	169.240 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	16

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

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	71.680 Å
R factor r_factor	0.1774
R_work r_work	0.1740
R_free r_free	0.2385

Description description	NADP-dependent isopropanol dehydrogenase
Molecular weight formula_weight	37912.2 kDa
EC 编号 ec_number	1.1.1.80
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	10622

NADH-dependent variant of TBADH

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

NADP-dependent isopropanol dehydrogenase

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Thermoanaerobacter brockii
NCBI Class编号 ncbi_taxonomy_id	29323
宿主生物 host_organism	Escherichia coli

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

fit	/app/data/saxs_computation/sd/6sdm/6sdm.fit
pddf	/app/data/pr_computation/sd/6sdm/6sdm.pr.out
profile	/app/data/saxs_computation/sd/6sdm/6sdm.dat