SAXSdb — 2qm4

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

Non-homologous end-joining factor 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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–233 Chain B； UniProt 1–233	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；23% PEG 6000, 0.1M Bis-Tris-Propane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K	Resolution 2.30 Å R-free 0.239
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–233 Chain D； UniProt 1–233	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；23% PEG 6000, 0.1M Bis-Tris-Propane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K	Resolution 2.30 Å R-free 0.239

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 2QM4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2R9A Crystal structure of human XLF Deposited 2007-09-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–224（224 aa） Fragment：N-terminal fragment, unp residues 1-224 Chain B 1–224（224 aa） Fragment：N-terminal fragment, unp residues 1-224	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；273 K；pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 2.50 Å R-free 0.287
3Q4F Crystal structure of xrcc4/xlf-cernunnos complex Deposited 2010-12-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–224（224 aa） Fragment：unp residues 1-224 Chain B 1–224（224 aa） Fragment：unp residues 1-224	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；9% v/v MPD, 50 mM MgSO4, 0.1 M Na Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 5.50 Å R-free 0.309
3Q4F Crystal structure of xrcc4/xlf-cernunnos complex Deposited 2010-12-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–224（224 aa） Fragment：unp residues 1-224 Chain F 1–224（224 aa） Fragment：unp residues 1-224	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；9% v/v MPD, 50 mM MgSO4, 0.1 M Na Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 5.50 Å R-free 0.309
3RWR Crystal structure of the human XRCC4-XLF complex Deposited 2011-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain D 1–224（224 aa） Fragment：unp residues 1-224 Chain E 1–224（224 aa） Fragment：unp residues 1-224 Chain H 1–224（224 aa） Fragment：unp residues 1-224 Chain I 1–224（224 aa） Fragment：unp residues 1-224	Not recorded	TBR HEXATANTALUM DODECABROMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；1.8M Ammonium citrate, pH 8.0, 20 mM Barium chloride dihydrate, 400 mM sodium thiocyanate, 0.5 mM tantalum bromide, 60% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.94 Å R-free 0.326
3SR2 Crystal Structure of Human XLF-XRCC4 Complex Deposited 2011-07-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 1–224（224 aa） Fragment：UNP Residues 1-224 Chain D 1–224（224 aa） Fragment：UNP Residues 1-224 Chain G 1–224（224 aa） Fragment：UNP Residues 1-224 Chain H 1–224（224 aa） Fragment：UNP Residues 1-224	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；303.15 K；protein combined with equal volumes of 100 mM HEPES, pH 7.8, 13% (w/v) PEG 3350, 300 mM NaCl, 2 mM ADP, 7 mM NaF and 3 mM BeCl) and then dehydrated over 1000 ul of 19% PEG 3350, 300 mM NaCl, 100 mM HEPES, pH7.8 under argon., vapor diffusion, temperature 303.15K	Resolution 3.97 Å R-free 0.369
3SR2 Crystal Structure of Human XLF-XRCC4 Complex Deposited 2011-07-06	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–224（224 aa） Fragment：UNP Residues 1-224 Chain D 1–224（224 aa） Fragment：UNP Residues 1-224	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；303.15 K；protein combined with equal volumes of 100 mM HEPES, pH 7.8, 13% (w/v) PEG 3350, 300 mM NaCl, 2 mM ADP, 7 mM NaF and 3 mM BeCl) and then dehydrated over 1000 ul of 19% PEG 3350, 300 mM NaCl, 100 mM HEPES, pH7.8 under argon., vapor diffusion, temperature 303.15K	Resolution 3.97 Å R-free 0.369
3SR2 Crystal Structure of Human XLF-XRCC4 Complex Deposited 2011-07-06	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 1–224（224 aa） Fragment：UNP Residues 1-224 Chain H 1–224（224 aa） Fragment：UNP Residues 1-224	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；303.15 K；protein combined with equal volumes of 100 mM HEPES, pH 7.8, 13% (w/v) PEG 3350, 300 mM NaCl, 2 mM ADP, 7 mM NaF and 3 mM BeCl) and then dehydrated over 1000 ul of 19% PEG 3350, 300 mM NaCl, 100 mM HEPES, pH7.8 under argon., vapor diffusion, temperature 303.15K	Resolution 3.97 Å R-free 0.369
3W03 XLF-XRCC4 complex Deposited 2012-10-17	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–233（233 aa） Fragment：UNP residues 1-233 Chain B 1–233（233 aa） Fragment：UNP residues 1-233	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1M Tris pH7.5, 2M Sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 8.49 Å R-free 0.360
6ERG Complex of XLF and heterodimer Ku bound to DNA Deposited 2017-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain F 287–299（13 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；18% PEG 3350, 150 mM Na sulfate , 100 mM Bis-Tris-Propane	Resolution 2.90 Å R-free 0.244
6ERG Complex of XLF and heterodimer Ku bound to DNA Deposited 2017-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain C 287–299（13 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；18% PEG 3350, 150 mM Na sulfate , 100 mM Bis-Tris-Propane	Resolution 2.90 Å R-free 0.244
6ERH Complex of XLF and heterodimer Ku bound to DNA Deposited 2017-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain M 281–299（19 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；18% PEG 3350, 150 mM sodium sulfate, and 100 mM Bis-Tris-Propane	Resolution 2.80 Å R-free 0.252
6ERH Complex of XLF and heterodimer Ku bound to DNA Deposited 2017-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain T 281–299（19 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；18% PEG 3350, 150 mM sodium sulfate, and 100 mM Bis-Tris-Propane	Resolution 2.80 Å R-free 0.252
7LSY NHEJ Short-range synaptic complex Deposited 2021-02-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: heptadecameric	Chain H 1–299（299 aa） Chain I 1–299（299 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.40 Å
7LT3 NHEJ Long-range synaptic complex Deposited 2021-02-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric	Chain H 1–299（299 aa） Chain I 1–299（299 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
7NFC Cryo-EM structure of NHEJ super-complex (dimer) Deposited 2021-02-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric	Chain Q 1–299（299 aa） Chain R 1–299（299 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.14 Å
7NFE Cryo-EM structure of NHEJ super-complex (monomer) Deposited 2021-02-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain F 1–299（299 aa） Chain G 1–299（299 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.29 Å
7ZYG CryoEM structure of Ku heterodimer bound to DNA, PAXX and XLF Deposited 2022-05-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain F 1–299（299 aa）	Not recorded	PO4 PHOSPHATE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.68 Å
8BHV DNA-PK XLF mediated dimer bound to PAXX Deposited 2022-11-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric	Chain Q 1–299（299 aa） Chain R 1–299（299 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.51 Å
8BHY DNA-PK Ku80 mediated dimer bound to PAXX and XLF Deposited 2022-11-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric	Chain f 1–299（299 aa） Chain m 1–299（299 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.33 Å
8BOT Cryo-EM structure of NHEJ supercomplex(trimer) Deposited 2022-11-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 25-meric	Chain Q 1–299（299 aa） Chain R 1–299（299 aa） Chain X 1–299（299 aa） Chain Y 1–299（299 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.76 Å
8EZA NHEJ Long-range complex with PAXX Deposited 2022-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric	Chain H 1–299（299 aa） Chain I 1–299（299 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.39 Å
8EZB NHEJ Long-range complex with ATP Deposited 2022-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric	Chain H 1–299（299 aa） Chain I 1–299（299 aa）	Not recorded	MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.90 Å
9CQ3 The gap-filling complex with Pol mu engaged in the NHEJ pathway Deposited 2024-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric	Chain C 1–299（299 aa） Chain c 1–299（299 aa）	Not recorded	MG MAGNESIUM ION × 2 DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9CQ6 The ligation complex in the NHEJ pathway Deposited 2024-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric	Chain C 1–299（299 aa） Chain c 1–299（299 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9CQC The ligation complex like in the NHEJ pathway Deposited 2024-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric	Chain C 1–299（299 aa） Chain c 1–299（299 aa）	Not recorded	DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9IAX DNA-PK, LX4, XLF - Catalytic domain of L4 Deposited 2025-02-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain D 1–299（299 aa） Chain M 1–299（299 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.97 Å
9IOL Cryo-EM structure of the complex of DNA, Ku70/80, and laXLF. Deposited 2024-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain M 287–299（13 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 2OP (2S)-2-HYDROXYPROPANOIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
9N81 A gap-filling complex with Pol mu engaged in the NHEJ Pathway Deposited 2025-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric	Chain C 1–299（299 aa） Chain c 1–299（299 aa）	Not recorded	MG MAGNESIUM ION × 1 DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9N82 The ligation (AMP-Lys) complex in the NHEJ pathway Deposited 2025-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric	Chain C 1–299（299 aa） Chain c 1–299（299 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9N83 The ligation complex in the NHEJ pathway Deposited 2025-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric	Chain C 1–299（299 aa） Chain c 1–299（299 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

25 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NHEJ1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–235； UniProt 1–233 Author chain B； PDBConstruct 3–235； UniProt 1–233 Author chain C； PDBConstruct 3–235； UniProt 1–233 Author chain D； PDBConstruct 3–235； UniProt 1–233

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	2qm4
Deposition date deposition_date	2007-07-14
Structure title title	Crystal structure of human XLF/Cernunnos, a non-homologous end-joining factor
Keywords keywords	XRCC4 like factor, homodimer, beta-sandwich, coiled-coil, Recombination; RECOMBINATION
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	37.76 Å
Radius of gyration Rg (electron density) rg_electron	37.78 Å
Forward intensity I(0) i0	166498000.00
Molecular weight molecular_weight	103170.0 kDa
Excluded volume excluded_volume	128150 Å³
Envelope volume envelope_volume	173380 Å³
Hydration-shell volume shell_volume	40619 Å³
Envelope diameter envelope_diameter	145.9 Å
Shell Rg shell_rg	40.71 Å
Envelope Rg envelope_rg	38.16 Å
Shape Rg shape_rg	37.86 Å
Total Rg total_rg	37.71 Å
Total atoms total_atoms	7113
Residues n_residues	874
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	136.0 Å
Rg (real space) rg_real	38.09 Å
Rg uncertainty (real space) rg_real_error	1.53 Å
I(0) (real space) i0_real	1.6650e+08
I(0) uncertainty (real space) i0_real_error	3.1600e+06
Rg (reciprocal space) rg_reciprocal	37.89 Å
I(0) (reciprocal space) i0_reciprocal	166500000.0000
Solution quality estimate total_estimate	0.8449
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	42.1 Å
Skewness Skewness skewness	0.527
Kurtosis Kurtosis kurtosis	-0.117
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	21310000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.750; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.862; Smooth: 0.868

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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) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	2qm4A01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	210 — Dna Repair Protein Xrcc4; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — DNA double-strand break repair and VJ recombination XRCC4, N-terminal

Domain ID domain_id	2qm4A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	450 — Helix hairpin bin

Domain ID domain_id	2qm4B01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	210 — Dna Repair Protein Xrcc4; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — DNA double-strand break repair and VJ recombination XRCC4, N-terminal

Domain ID domain_id	2qm4B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	450 — Helix hairpin bin

Domain ID domain_id	2qm4C01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	210 — Dna Repair Protein Xrcc4; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — DNA double-strand break repair and VJ recombination XRCC4, N-terminal

Domain ID domain_id	2qm4C02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	450 — Helix hairpin bin

Domain ID domain_id	2qm4D01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	210 — Dna Repair Protein Xrcc4; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — DNA double-strand break repair and VJ recombination XRCC4, N-terminal

Domain ID domain_id	2qm4D02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	450 — Helix hairpin bin

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8. Citations (1)

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Unit-cell length a length_a	63.736 Å
Unit-cell length b length_b	92.913 Å
Unit-cell length c length_c	103.693 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.22 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	37.010 Å
R factor r_factor	0.1848
R_work r_work	0.1824
R_free r_free	0.2389

Description description	Non-homologous end-joining factor 1
Molecular weight formula_weight	27059.8 kDa
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	7510

Crystal structure of human XLF/Cernunnos, a non-homologous end-joining factor

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

Non-homologous end-joining factor 1

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 water

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	232

fit	/app/data/saxs_computation/qm/2qm4/2qm4.fit
pddf	/app/data/pr_computation/qm/2qm4/2qm4.pr.out
profile	/app/data/saxs_computation/qm/2qm4/2qm4.dat