SAXSdb — 9qv9

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1. Structure Basics

entry_id	9qv9
deposition_date	2025-04-11
last_revision	2025-10-29
title	apPol-DNA-nucleotide complex (ternary 3)
keywords	DNA polymerase, REPLICATION; REPLICATION
method	ELECTRON MICROSCOPY

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Download Data

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

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2. SAXS Parameters (CRYSOL)

rg_guinier	31.07 Å
rg_electron	30.15 Å
i0	134297000.00
molecular_weight	86022.0 kDa
excluded_volume	105160 Å³
envelope_volume	139720 Å³
shell_volume	38630 Å³
envelope_diameter	103.2 Å
shell_rg	37.23 Å
envelope_rg	30.43 Å
shape_rg	30.12 Å
total_rg	30.82 Å
total_atoms	6006
n_residues	661
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

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3. P(r) Analysis (GNOM)

dmax	96.4 Å
rg_real	31.01 Å
rg_real_error	0.63 Å
i0_real	1.3430e+08
i0_real_error	1.8140e+06
rg_reciprocal	31.04 Å
i0_reciprocal	134300000.0000
total_estimate	0.9017
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	35.9 Å
skewness	0.258
kurtosis	-0.481
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	17610000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.836

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Plastid replication-repair enzyme
formula_weight	76473.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6006

MGSSHHHHHHSQDPENLYFQGDEITKKYIKDNIINVDDNIIKKKDIFKLKNENNEITECAFEYFESKKKFDDDIESRFFIINDNNYNENINLIYKDIKYCGLNIQTTGLEVFDENIRLIQIAVENYPVIIYDMFNINKKDILDGLRKVLENKNIIKIIQNGKFDAKFLLHNNFKIENIFDTYIASKLLDKNKNMYGFKLNNIVEKYLNVILDKQQQNSVWNNSLLNNNQLFYAARDSSCLLKLYKKLKEEIKKENLHIVNDIENKCILPICDMELNGIKVDLENLQKSTNEILNELNIEKDNLKKKLKDENINVNSQQQVLKALQKNNVRDISNKLIENTSDSNLKNFLNHEEIISLRNYRRLYKLYSAFYLKLPLHINTKTNKIHTTFNQLKTFSGRFSSEKPNLQQIPRQKNIREIFIPNDNNIFIIADFKQIELKIAAEITNDEIMLKAYNNNIDLHTLTASIITKKNIPDINKEDRHIAKAINFGLIYGMNYVNLKNYANTYYGLNMSLDQCLYFYNSFFEHYKGIYKWHNQVKQKRALQYSTLSNRKVIFPYFSFTKALNYPVQGTCADILKLALVDLYDNLKDINGKIILCVHDEIIIEVNKKFQEEALKILVQSMENSASYFLKKVKCEVSVKIAENWGSKD

Source

organism	Plasmodium falciparum
common_name	malaria parasite P. falciparum
ncbi_taxonomy_id	5833
host_organism	Escherichia coli

Entity 2 polymer

description	DNA primer strand
formula_weight	7715.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

CAGGTGTCAGTCAGCTAGTGCTGAC

Entity 3 polymer

description	DNA template strand
formula_weight	11023.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	C

GCTACCGTAGCGTCAGCACTAGCTGACTGACACCTG

Entity 4 non-polymer

description	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.500 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.50 Å
resolution_method	—
num_particles	92787

fit	/app/data/saxs_computation/qv/9qv9/9qv9.fit
pddf	/app/data/pr_computation/qv/9qv9/9qv9.pr.out
profile	/app/data/saxs_computation/qv/9qv9/9qv9.dat

apPol-DNA-nucleotide complex (ternary 3)

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)