8bsc

CryoEM structure of the RAD51 nucleoprotein filament in the presence of ADP and Ca2+

Method: ELECTRON MICROSCOPY D_max: 176.1 Å Quality: GOOD

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

DNA repair protein RAD51 homolog 1

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 homooligomer Homooligomer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain A； UniProt 1–339 Chain B； UniProt 1–339 Chain C； UniProt 1–339 Chain D； UniProt 1–339 Chain E； UniProt 1–339 Chain F； UniProt 1–339 Chain G； UniProt 1–339	Not recorded	CA CALCIUM ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 7	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.60 Å

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 8BSC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B22 RAD51 (N-TERMINAL DOMAIN) Deposited 1998-12-04	Different construct Different mutation/modification Different oligomeric state 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 1–114（114 aa） Fragment：N-TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 100mM NACL；Pressure 1	Resolution not provided
1N0W Crystal structure of a RAD51-BRCA2 BRC repeat complex Deposited 2002-10-15	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 × 4 PDB declaration: tetrameric	Chain A 97–339（243 aa） Fragment：ATPase domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；ETHYLENE GLYCOL, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.70 Å R-free 0.206
5H1B Human RAD51 presynaptic complex Deposited 2016-10-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: tetrameric	Chain A 1–339（339 aa） Chain B 1–339（339 aa） Chain C 1–339（339 aa）	Mutation：K313Q Mutation：K313Q Mutation：K313Q	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25mM Tris-HCl, pH 7.5, 50mM KCl, 1mM dithiothreitol, 1mM AMP-PNP and 2mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
5H1C Human RAD51 post-synaptic complexes Deposited 2016-10-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: pentameric	Chain A 1–339（339 aa） Chain B 1–339（339 aa） Chain C 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25mM Tris-HCl, pH 7.5, 50mM KCl, 1mM dithiothreitol, 1mM AMP-PNP and 2mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
5JZC helical filament Deposited 2016-05-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 1–339（339 aa） Chain B 1–339（339 aa） Chain C 1–339（339 aa） Chain D 1–339（339 aa） Chain E 1–339（339 aa） Chain F 1–339（339 aa） Chain G 1–339（339 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7	Resolution 4.20 Å
5NP7 CryoEM structure of Human Rad51 on single-stranded DNA to 4.2A resolution. Deposited 2017-04-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 1–339（339 aa） Chain B 1–339（339 aa） Chain C 1–339（339 aa） Chain D 1–339（339 aa） Chain E 1–339（339 aa） Chain F 1–339（339 aa） Chain G 1–339（339 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 4.20 Å
5NWL Crystal structure of a human RAD51-ATP filament. Deposited 2017-05-06	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 1–339（339 aa） Chain B 1–339（339 aa） Chain C 1–339（339 aa） Chain D 1–339（339 aa） Chain E 1–339（339 aa） Chain F 1–339（339 aa） Chain G 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 MES pH 5.2 MPD	Resolution 3.93 Å R-free 0.317
5NWL Crystal structure of a human RAD51-ATP filament. Deposited 2017-05-06	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain H 1–339（339 aa） Chain I 1–339（339 aa） Chain J 1–339（339 aa） Chain K 1–339（339 aa） Chain L 1–339（339 aa） Chain M 1–339（339 aa） Chain N 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 MES pH 5.2 MPD	Resolution 3.93 Å R-free 0.317
7C9A Human RAD51 post-synaptic complexes mutant (V273P, D274G) Deposited 2020-06-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: pentameric	Chain A 1–339（339 aa） Chain B 1–339（339 aa） Chain C 1–339（339 aa）	Mutation：V273P, D274G Mutation：V273P, D274G Mutation：V273P, D274G	CA CALCIUM ION × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM Tris-HCl, pH 7.5, 50 mM KCl and 1 mM dithiothreitol) containing 2 mM AMP-PNP and 5 mM CaCl2 cryo-EM vitrification conditions Cryogen ETHANE；The grids were blotted for 1 sec at 22 degree C with 100% relative humidity and plunge-frozen in liquid ethane cooled by liquid nitrogen using a Vitrobot Mark IV (Thermo Fisher).	Resolution 3.43 Å
7EJC human RAD51 presynaptic complex Deposited 2021-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: tetrameric	Chain A 1–339（339 aa） Chain B 1–339（339 aa） Chain C 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 3 J46 4-bromanyl-N-(4-bromophenyl)-3-[(phenylmethyl)sulfamoyl]benzamide × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.97 Å
7EJE human RAD51 post-synaptic complex Deposited 2021-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: pentameric	Chain A 1–339（339 aa） Chain B 1–339（339 aa） Chain C 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.98 Å
8BQ2 CryoEM structure of the pre-synaptic RAD51 nucleoprotein filament in the presence of ATP and Ca2+ Deposited 2022-11-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 9 PDB declaration: decameric	Chain A 1–339（339 aa） Chain B 1–339（339 aa） Chain C 1–339（339 aa） Chain D 1–339（339 aa） Chain E 1–339（339 aa） Chain F 1–339（339 aa） Chain G 1–339（339 aa） Chain H 1–339（339 aa） Chain I 1–339（339 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 9 CA CALCIUM ION × 18	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8BR2 CryoEM structure of the post-synaptic RAD51 nucleoprotein filament in the presence of ATP and Ca2+ Deposited 2022-11-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: octameric	Chain A 1–339（339 aa） Chain B 1–339（339 aa） Chain C 1–339（339 aa） Chain D 1–339（339 aa） Chain E 1–339（339 aa） Chain F 1–339（339 aa）	Not recorded	CA CALCIUM ION × 12 ATP ADENOSINE-5'-TRIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8GYK CryoEM structure of the RAD51_ADP filament Deposited 2022-09-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–339（339 aa） Chain B 1–339（339 aa） Chain C 1–339（339 aa） Chain D 1–339（339 aa） Chain E 1–339（339 aa） Chain F 1–339（339 aa） Chain G 1–339（339 aa） Chain H 1–339（339 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 8 MG MAGNESIUM ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å
8JND The cryo-EM structure of the nonameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-06-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 19-meric	Chain K 1–339（339 aa） Chain L 1–339（339 aa） Chain M 1–339（339 aa） Chain N 1–339（339 aa） Chain O 1–339（339 aa） Chain P 1–339（339 aa） Chain Q 1–339（339 aa） Chain R 1–339（339 aa） Chain S 1–339（339 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.66 Å
8JNE The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome without the linker DNA binding Deposited 2023-06-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric	Chain K 1–339（339 aa） Chain L 1–339（339 aa） Chain M 1–339（339 aa） Chain N 1–339（339 aa） Chain O 1–339（339 aa） Chain P 1–339（339 aa） Chain Q 1–339（339 aa） Chain R 1–339（339 aa） Chain S 1–339（339 aa） Chain T 1–339（339 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.68 Å
8JNF The cryo-EM structure of the RAD51 filament bound to the nucleosome Deposited 2023-06-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric	Chain K 1–339（339 aa） Chain L 1–339（339 aa） Chain M 1–339（339 aa） Chain N 1–339（339 aa） Chain O 1–339（339 aa） Chain P 1–339（339 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.91 Å
8PBC RAD51 filament on ssDNA bound by the BRCA2 c-terminus Deposited 2023-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 22-meric	Chain A 1–339（339 aa） Chain B 1–339（339 aa） Chain C 1–339（339 aa） Chain D 1–339（339 aa） Chain E 1–339（339 aa） Chain F 1–339（339 aa） Chain G 1–339（339 aa） Chain H 1–339（339 aa） Chain I 1–339（339 aa） Chain J 1–339（339 aa） Chain K 1–339（339 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 11 CA CALCIUM ION × 22	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.61 Å
8PBD RAD51 filament on dsDNA bound by the BRCA2 c-terminus Deposited 2023-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric	Chain A 1–339（339 aa） Chain B 1–339（339 aa） Chain C 1–339（339 aa） Chain D 1–339（339 aa） Chain E 1–339（339 aa） Chain F 1–339（339 aa） Chain G 1–339（339 aa） Chain H 1–339（339 aa） Chain I 1–339（339 aa） Chain J 1–339（339 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 10 CA CALCIUM ION × 20	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.83 Å
8R64 Cryo-EM structure of the FIGNL1 AAA hexamer bound to RAD51 Deposited 2023-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain G 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8RCD RAD51 nucleoprotein filament on abasic single-stranded DNA Deposited 2023-12-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 8 PDB declaration: nonameric	Chain A 1–339（339 aa） Chain B 1–339（339 aa） Chain C 1–339（339 aa） Chain D 1–339（339 aa） Chain E 1–339（339 aa） Chain F 1–339（339 aa） Chain G 1–339（339 aa） Chain H 1–339（339 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 8 CA CALCIUM ION × 16	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8RCF RAD51 nucleoprotein filament on double-stranded abasic DNA Deposited 2023-12-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 8 PDB declaration: decameric	Chain A 1–339（339 aa） Chain B 1–339（339 aa） Chain C 1–339（339 aa） Chain D 1–339（339 aa） Chain E 1–339（339 aa） Chain F 1–339（339 aa） Chain G 1–339（339 aa） Chain H 1–339（339 aa）	Not recorded	CA CALCIUM ION × 16 ATP ADENOSINE-5'-TRIPHOSPHATE × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8UVW Crystal structure of RAD51-BRCA2 Cter complex Deposited 2023-11-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 85–339（255 aa） Chain D 97–339（243 aa）	Mutation：C319S Mutation：S208E,A209D,C3287A,C3304A,C391S	ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% v/v 1,4-Dioxane 0.05 M MOPS pH 7.0 0.005 M Magnesium chloride hexahydrate 0.001 M Spermine	Resolution 2.73 Å R-free 0.282
8XBT The cryo-EM structure of the octameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric	Chain K 1–339（339 aa） Chain L 1–339（339 aa） Chain M 1–339（339 aa） Chain N 1–339（339 aa） Chain O 1–339（339 aa） Chain P 1–339（339 aa） Chain Q 1–339（339 aa） Chain R 1–339（339 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.12 Å
8XBU The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric	Chain K 1–339（339 aa） Chain L 1–339（339 aa） Chain M 1–339（339 aa） Chain N 1–339（339 aa） Chain O 1–339（339 aa） Chain P 1–339（339 aa） Chain Q 1–339（339 aa） Chain R 1–339（339 aa） Chain S 1–339（339 aa） Chain T 1–339（339 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.24 Å
8XBV The cryo-EM structure of the RAD51 L1 and L2 loops bound to the linker DNA with the sticky end of the nucleosome Deposited 2023-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain K 1–339（339 aa） Chain L 1–339（339 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.61 Å
8XBW The cryo-EM structure of the RAD51 N-terminal lobe domain bound to the histone H4 tail of the nucleosome Deposited 2023-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain L 1–339（339 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.89 Å
8XBX The cryo-EM structure of the RAD51 L2 loop bound to the linker DNA with the blunt end of the nucleosome Deposited 2023-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: pentameric	Chain K 1–339（339 aa） Chain L 1–339（339 aa） Chain M 1–339（339 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.36 Å
8XBY The cryo-EM structure of the RAD51 L1 and L2 loops bound to the linker DNA with the blunt end of the nucleosome Deposited 2023-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: pentameric	Chain K 1–339（339 aa） Chain L 1–339（339 aa） Chain M 1–339（339 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.80 Å
9I62 CryoEM structure of a RAD51 D-loop Deposited 2025-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 9 PDB declaration: 12-meric	Chain A 1–339（339 aa） Chain B 1–339（339 aa） Chain C 1–339（339 aa） Chain D 1–339（339 aa） Chain E 1–339（339 aa） Chain F 1–339（339 aa） Chain G 1–339（339 aa） Chain H 1–339（339 aa） Chain I 1–339（339 aa）	Not recorded	CA CALCIUM ION × 18 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.64 Å
9OMY Cryo-EM structure of an octameric RAD51-XRCC3-RAD51C (RAD51-X3C) complex Deposited 2025-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–339（339 aa） Chain B 1–339（339 aa） Chain D 1–339（339 aa） Chain E 1–339（339 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.25 Å
9OMZ Cryo-EM structure of a pentameric RAD51-XRCC3-RAD51C-RAD51D-XRCC2 (51-X3CDX2) complex. Deposited 2025-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–339（339 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.51 Å
9Q23 DX2-CX3-RAD51 structure in the intermediate state Deposited 2025-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: heptameric	Chain G 1–339（339 aa） Chain I 1–339（339 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.84 Å
9Q25 DX2-CX3-RAD51 in the closed state Deposited 2025-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: hexameric	Chain G 1–339（339 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.24 Å
9Q28 DX2-CX3-RAD51 in the active state Deposited 2025-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: heptameric	Chain G 1–339（339 aa） Chain I 1–339（339 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.84 Å
9Q29 DX2-CX3 structure capping RAD51 filament Deposited 2025-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: decameric	Chain G 1–339（339 aa） Chain I 1–339（339 aa） Chain J 1–339（339 aa） Chain K 1–339（339 aa） Chain L 1–339（339 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 CA CALCIUM ION × 13 ATP ADENOSINE-5'-TRIPHOSPHATE × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.61 Å
9Q2A BCDX2-CX3-RAD51-RAD51-ssDNA supercomplex Deposited 2025-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: nonameric	Chain G 1–339（339 aa） Chain I 1–339（339 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.67 Å
9Q2B DX2-CX3-RAD51 bound to DNA bubble Deposited 2025-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain G 1–339（339 aa） Chain I 1–339（339 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 4 ATP ADENOSINE-5'-TRIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9QN8 RAD51 filament in complex with calcium and ATP bound by the RAD51AP1 C-terminus Deposited 2025-03-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 13-meric	Chain A 1–339（339 aa） Chain C 1–339（339 aa） Chain E 1–339（339 aa） Chain G 1–339（339 aa） Chain I 1–339（339 aa） Chain K 1–339（339 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 7 CA CALCIUM ION × 7 K POTASSIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å
9QNA RAD51 filament in complex with magnesium and ATP Deposited 2025-03-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: heptameric	Chain A 1–339（339 aa） Chain C 1–339（339 aa） Chain E 1–339（339 aa） Chain G 1–339（339 aa） Chain I 1–339（339 aa） Chain K 1–339（339 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 6 K POTASSIUM ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.26 Å
9QNB RAD51 filament in complex with magnesium and ADP Deposited 2025-03-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–339（339 aa） Chain C 1–339（339 aa） Chain E 1–339（339 aa） Chain G 1–339（339 aa） Chain I 1–339（339 aa） Chain K 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 6 K POTASSIUM ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.63 Å
9QNC RAD51 filament in complex with magnesium and ATP bound by the RAD51AP1 C-terminus Deposited 2025-03-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 13-meric	Chain A 1–339（339 aa） Chain C 1–339（339 aa） Chain E 1–339（339 aa） Chain G 1–339（339 aa） Chain I 1–339（339 aa） Chain K 1–339（339 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 7 K POTASSIUM ION × 5 MG MAGNESIUM ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.98 Å
9SRZ RAD51-ssDNA filament in complex with calcium and ATP bound by the RAD54B N-terminus Deposited 2025-09-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 13-meric	Chain I 1–339（339 aa） Chain J 1–339（339 aa） Chain K 1–339（339 aa） Chain L 1–339（339 aa） Chain M 1–339（339 aa） Chain N 1–339（339 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 6 CA CALCIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.61 Å
9SSL RAD51-ssDNA filament in complex with magnesium and ATP bound by the RAD54B N-terminus (peptide) Deposited 2025-09-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 13-meric	Chain A 1–339（339 aa） Chain B 1–339（339 aa） Chain C 1–339（339 aa） Chain D 1–339（339 aa） Chain E 1–339（339 aa） Chain F 1–339（339 aa）	Not recorded	K POTASSIUM ION × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9SVX XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filament on single stranded DNA Deposited 2025-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: decameric	Chain E 1–339（339 aa） Chain F 1–339（339 aa） Chain G 1–339（339 aa） Chain H 1–339（339 aa） Chain I 1–339（339 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 8 ATP ADENOSINE-5'-TRIPHOSPHATE × 7 CA CALCIUM ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM HEPES-NaOH pH 7.5, 100 mM NaCl, 2.5 mM MgCl2, 2.5 mM CaCl2, 1 mM ATP, 0.25 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
9SVY XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filament on partially duplex DNA Deposited 2025-10-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric	Chain E 1–339（339 aa） Chain F 1–339（339 aa） Chain G 1–339（339 aa） Chain H 1–339（339 aa） Chain I 1–339（339 aa） Chain J 1–339（339 aa） Chain K 1–339（339 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 9 MG MAGNESIUM ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 1 CA CALCIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM HEPES-NaOH pH 7.5, 100 mM NaCl, 2.5 mM MgCl2, 2.5 mM CaCl2, 1 mM ATP, 0.25 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
9SW0 XRCC3-RAD51C-RAD51D-XRCC2 (XRCC3 complex) capping a RAD51 filament on a D-loop intermediate Deposited 2025-10-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric	Chain E 1–339（339 aa） Chain F 1–339（339 aa） Chain G 1–339（339 aa） Chain H 1–339（339 aa） Chain I 1–339（339 aa） Chain J 1–339（339 aa） Chain K 1–339（339 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 8 CA CALCIUM ION × 7 MG MAGNESIUM ION × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM HEPES-NaOH pH 7.5, 100 mM NaCl, 2.5 mM MgCl2, 2.5 mM CaCl2, 1 mM ATP, 0.25 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9TRL RAD51-ssDNA filament in complex with magnesium and ATP bound by the RAD54B N-terminus (beta-barrel) Deposited 2025-12-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 12-meric	Chain A 1–339（339 aa） Chain B 1–339（339 aa） Chain C 1–339（339 aa） Chain D 1–339（339 aa） Chain E 1–339（339 aa） Chain F 1–339（339 aa）	Not recorded	K POTASSIUM ION × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9TRM RAD51-dsDNA filament in complex with calcium and ATP bound by the RAD54B N-terminus Deposited 2025-12-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric	Chain I 1–339（339 aa） Chain J 1–339（339 aa） Chain K 1–339（339 aa） Chain L 1–339（339 aa） Chain M 1–339（339 aa） Chain N 1–339（339 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 6 CA CALCIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.40 Å
9TYY RAD51-ssDNA filament in complex with calcium and ATP bound by the RAD54 N-terminus Deposited 2026-01-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 13-meric	Chain I 1–339（339 aa） Chain J 1–339（339 aa） Chain K 1–339（339 aa） Chain L 1–339（339 aa） Chain M 1–339（339 aa） Chain N 1–339（339 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 6 CA CALCIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9ZZR Cryo-EM Structure of a RAD51 filament bound by ssDNA and the XRCC3-RAD51C-RAD51D-XRCC2 paralog complex Deposited 2026-01-07	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: dodecameric	Chain E 22–338（317 aa） Chain F 24–337（314 aa） Chain K 22–338（317 aa） Chain O 22–338（317 aa） Chain R 22–337（316 aa） Chain V 22–337（316 aa） Chain W 22–338（317 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å

50 other PDB entries and 51 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RAD51_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–339； UniProt 1–339 Author chain B； PDBConstruct 1–339； UniProt 1–339 Author chain C； PDBConstruct 1–339； UniProt 1–339 Author chain D； PDBConstruct 1–339； UniProt 1–339 Author chain E； PDBConstruct 1–339； UniProt 1–339 Author chain F； PDBConstruct 1–339； UniProt 1–339 Author chain G； PDBConstruct 1–339； UniProt 1–339

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8bsc
Deposition date deposition_date	2022-11-24
Structure title title	CryoEM structure of the RAD51 nucleoprotein filament in the presence of ADP and Ca2+
Keywords keywords	DNA repair, Homologous Recombination, DNA-strand exchange, ATPase, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	51.80 Å
Radius of gyration Rg (electron density) rg_electron	51.68 Å
Forward intensity I(0) i0	884339000.00
Molecular weight molecular_weight	242500.0 kDa
Excluded volume excluded_volume	301770 Å³
Envelope volume envelope_volume	438410 Å³
Hydration-shell volume shell_volume	71284 Å³
Envelope diameter envelope_diameter	184.1 Å
Shell Rg shell_rg	55.29 Å
Envelope Rg envelope_rg	50.26 Å
Shape Rg shape_rg	51.68 Å
Total Rg total_rg	51.81 Å
Total atoms total_atoms	16982
Residues n_residues	2191
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	176.1 Å
Rg (real space) rg_real	51.92 Å
Rg uncertainty (real space) rg_real_error	2.01 Å
I(0) (real space) i0_real	8.8430e+08
I(0) uncertainty (real space) i0_real_error	1.8320e+07
Rg (reciprocal space) rg_reciprocal	51.67 Å
I(0) (reciprocal space) i0_reciprocal	884000000.0000
Solution quality estimate total_estimate	0.8513
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.1 Å
Skewness Skewness skewness	0.296
Kurtosis Kurtosis kurtosis	-0.650
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	188200000.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.801; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.706

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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	DNA repair protein RAD51 homolog 1
Molecular weight formula_weight	37009.1 kDa
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,A,B,C,E,F,G
Atom count atom_count	17059

MAMQMQLEANADTSVEEESFGPQPISRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILAEAAKLVPMGFTTATEFHQRRSEIIQITTGSKELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLLAVAERYGLSGSDVLDNVAYARAFNTDHQTQLLYQASAMMVESRYALLIVDSATALYRTDYSGRGELSARQMHLARFLRMLLRLADEFGVAVVITNQVVAQVDGAAMFAADPKKPIGGNIIAHASTTRLYLRKGRGETRICKIYDSPCLPEAEAMFAINADGVGDAKD

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	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	7

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8. Citations (1)

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Resolution resolution	3.60 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	40481

fit	/app/data/saxs_computation/bs/8bsc/8bsc.fit
pddf	/app/data/pr_computation/bs/8bsc/8bsc.pr.out
profile	/app/data/saxs_computation/bs/8bsc/8bsc.dat