← Back to search

9rdi

Crystal Structure of Flap Endonuclease FEN1 with Compound 5

Method: X-RAY DIFFRACTION D_max: 96.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9rdi
deposition_date	2025-06-02
title	Crystal Structure of Flap Endonuclease FEN1 with Compound 5
keywords	Endonuclease, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	30.76 Å
rg_electron	30.03 Å
i0	290309000.00
molecular_weight	79936.0 kDa
excluded_volume	67784 Å³
envelope_volume	120990 Å³
shell_volume	34336 Å³
envelope_diameter	102.3 Å
shell_rg	36.37 Å
envelope_rg	29.44 Å
shape_rg	29.61 Å
total_rg	30.91 Å
total_atoms	5248
n_residues	622
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

▼

3. P(r) Analysis (GNOM)

dmax	96.3 Å
rg_real	30.83 Å
rg_real_error	0.77 Å
i0_real	2.9030e+08
i0_real_error	4.9360e+06
rg_reciprocal	30.80 Å
i0_reciprocal	290300000.0000
total_estimate	0.8691
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.6 Å
skewness	0.349
kurtosis	-0.462
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	7136000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.529

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	Flap endonuclease 1
formula_weight	38642.4 kDa
ec_number	3.1.-.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5332

MGIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTLEVLFQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	2-methyl-9-oxidanyl-6-(phenylmethyl)-3,4-dihydropyrazino[1,2-c]pyrimidine-1,8-dione
formula_weight	285.3 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	6-tungstotellurate(VI)
formula_weight	1614.6 kDa
src_method	syn
entity_count	9

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	4

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	53

▶

6. Citations (1)

▶

length_a	61.453 Å
length_b	116.150 Å
length_c	139.706 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.105 Å
resolution_low	40.410 Å
r_factor	0.2123
r_work	0.2113
r_free	0.2319

fit	/app/data/saxs_computation/rd/9rdi/9rdi.fit
pddf	/app/data/pr_computation/rd/9rdi/9rdi.pr.out
profile	/app/data/saxs_computation/rd/9rdi/9rdi.dat