← Back to search

13yf

PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3Dpol in complex with Z1563512128

Method: X-RAY DIFFRACTION D_max: 70.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	13yf
deposition_date	2026-03-06
last_revision	2026-03-18
title	PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3Dpol in complex with Z1563512128
keywords	SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, RNA-dependent RNA polymerase, TRANSFERASE; TRANSFERASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	24.16 Å
rg_electron	23.02 Å
i0	43730000.00
molecular_weight	52984.0 kDa
excluded_volume	67136 Å³
envelope_volume	82523 Å³
shell_volume	29155 Å³
envelope_diameter	73.8 Å
shell_rg	30.66 Å
envelope_rg	22.82 Å
shape_rg	23.01 Å
total_rg	24.00 Å
total_atoms	3727
n_residues	457
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	70.6 Å
rg_real	23.95 Å
rg_real_error	0.29 Å
i0_real	4.3730e+07
i0_real_error	5.4280e+05
rg_reciprocal	24.00 Å
i0_reciprocal	43730000.0000
total_estimate	0.9122
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	69.5 Å
skewness	0.005
kurtosis	-0.590
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	11400000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.995

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (7)

Entity 1 polymer

description	3Dpol RNA Dependent RNA Polymerase
formula_weight	52958.3 kDa
ec_number	3.4.22.29,3.6.1.15,3.4.22.28,2.7.7.48
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4052

GEIVSNEKSGVCINAPAKTKLQPSVFHQVFEGSKEPAVLNSKDPRLKTDFEEAIFSKYTGNKIMLMDEYMEEAVDHYVGCLEPLDISVDPIPLESAMYGMDGLEALDLTTSAGFPYLLQGKKKRDIFNRHTRDTTEMTKMLEKYGVDLPFVTFVKDELRSKEKVEKGKSRLIEASSLNDSVAMRVAFGNLYATFHSNPGTATGSAVGCDPDIFWSKIPILLDGEIFAFDYTGYDASLSPVWFACLKKVLIKLGYTHQTSFIDYLCHSVHLYKDRKYIVNGGMPSGSSGTSIFNTMINNIIIRTLLIRVYKGIDLDQFKMIAYGDDVIASYPHKIDPALLAEAGKHYGLVMTPADKGTSFVDTNWENVTFLKRYFRADDQYPFLIHPVMPMKEIHESIRWTKDPRNTQDHVRSLCYLAWHNGEEAYNEFCRKIRSVPVGRALTLPAYSSLRRKWLDSFGSSGHHHHHH

Source

organism	enterovirus D68
ncbi_taxonomy_id	42789
host_organism	Escherichia coli

Entity 2 non-polymer

description	ISOPROPYL ALCOHOL
formula_weight	60.1 kDa
src_method	syn
entity_count	15

Entity 3 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	N-[(2S)-2-hydroxypropyl]-N'-phenylurea
formula_weight	194.2 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	325

▶

6. Citations (1)

▶

length_a	55.312 Å
length_b	83.067 Å
length_c	58.594 Å
angle_alpha	90.00 °
angle_beta	108.63 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.450 Å
resolution_low	41.570 Å
r_factor	0.1810
r_work	0.1797
r_free	0.2066

fit	/app/data/saxs_computation/3y/13yf/13yf.fit
pddf	/app/data/pr_computation/3y/13yf/13yf.pr.out
profile	/app/data/saxs_computation/3y/13yf/13yf.dat