SciA(H42A) endonuclease from Escherichia phage T5 in complex with 10 bp DNA (GCGC sequence 1)

entry_id	9qgx
deposition_date	2025-03-14
last_revision	2026-03-25
title	SciA(H42A) endonuclease from Escherichia phage T5 in complex with 10 bp DNA (GCGC sequence 1)
keywords	HNH endonuclease, His-Me endonuclease, bacteriophage T5, nicked genome, DNA BINDING PROTEIN; DNA BINDING PROTEIN
method	X-RAY DIFFRACTION

rg_guinier	18.07 Å
rg_electron	17.34 Å
i0	11133500.00
molecular_weight	20505.0 kDa
excluded_volume	23810 ų
envelope_volume	29685 ų
shell_volume	14983 ų
envelope_diameter	66.8 Å
shell_rg	22.58 Å
envelope_rg	17.63 Å
shape_rg	17.29 Å
total_rg	18.19 Å
total_atoms	2643
n_residues	141
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	67.3 Å
rg_real	18.05 Å
rg_real_error	0.64 Å
i0_real	1.1130e+07
i0_real_error	1.3250e+05
rg_reciprocal	18.06 Å
i0_reciprocal	11130000.0000
total_estimate	0.8295
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.8 Å
skewness	0.351
kurtosis	-0.134
angular_range	— – 0.4400 Å−1
current_alpha	0.0000
highest_alpha	1796000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.632; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.901; Smooth: 0.994

Unit Cell

length_a	33.125 Å
length_b	72.122 Å
length_c	40.334 Å
angle_alpha	90.00 °
angle_beta	96.63 °
angle_gamma	90.00 °
z_pdb	2

Symmetry

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

Refinement

resolution	2.350 Å
resolution_low	32.900 Å
r_factor	0.2196
r_work	0.2169
r_free	0.2665

Diffraction

temperature

80.0 K

Files (7)

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

Curves (3)

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