SciA(H42Q) endonuclease from Escherichia phage T5 in complex with 10 bp DNA (GCGC sequence 2)

entry_id	9qgv
deposition_date	2025-03-14
last_revision	2026-03-25
title	SciA(H42Q) endonuclease from Escherichia phage T5 in complex with 10 bp DNA (GCGC sequence 2)
keywords	HNH endonuclease, His-Me endonuclease, bacteriophage T5, nicked genome, DNA BINDING PROTEIN; DNA BINDING PROTEIN
method	X-RAY DIFFRACTION

rg_guinier	17.84 Å
rg_electron	17.09 Å
i0	10719800.00
molecular_weight	20160.0 kDa
excluded_volume	23387 ų
envelope_volume	28940 ų
shell_volume	14794 ų
envelope_diameter	59.8 Å
shell_rg	22.35 Å
envelope_rg	17.18 Å
shape_rg	17.04 Å
total_rg	17.95 Å
total_atoms	2593
n_residues	139
n_harmonics	20
q_range	— – 0.5000 Å−1
n_points	101
shell_type	directional
solvent_density	0.3340 e/ų
contrast_shell	0.0300 e/ų
crysol_version	4.1.3

dmax	57.8 Å
rg_real	17.79 Å
rg_real_error	0.34 Å
i0_real	1.0720e+07
i0_real_error	1.2320e+05
rg_reciprocal	17.80 Å
i0_reciprocal	10720000.0000
total_estimate	0.8172
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	22.7 Å
skewness	0.262
kurtosis	-0.336
angular_range	— – 0.4450 Å−1
current_alpha	0.0000
highest_alpha	1444000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

Unit Cell

length_a	33.290 Å
length_b	71.690 Å
length_c	40.230 Å
angle_alpha	90.00 °
angle_beta	97.17 °
angle_gamma	90.00 °
z_pdb	2

Symmetry

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

Refinement

resolution	1.550 Å
resolution_low	35.840 Å
r_factor	0.2057
r_work	0.2041
r_free	0.2361

Diffraction

temperature

80.0 K

Files (7)

• pr_distribution /app/data/pr_computation/qg/9qgv/pr_distribution.json
• pr_output /app/data/pr_computation/qg/9qgv/9qgv.pr.out
• pr_plot /app/data/visualization/pr_computation/qg/9qgv/9qgv_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/qg/9qgv/9qgv.dat
• saxs_fit /app/data/saxs_computation/qg/9qgv/9qgv.fit
• saxs_log /app/data/saxs_computation/qg/9qgv/9qgv.log
• saxs_plot /app/data/visualization/saxs_computation/qg/9qgv/9qgv_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/qg/9qgv/9qgv.fit
pddf	/app/data/pr_computation/qg/9qgv/9qgv.pr.out
profile	/app/data/saxs_computation/qg/9qgv/9qgv.dat