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9xcf

Cryo-EM structure of csy3 with crRNA

Method: ELECTRON MICROSCOPY D_max: 299.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xcf
deposition_date	2025-10-25
title	Cryo-EM structure of csy3 with crRNA
keywords	CRISPR-Cas system, IMMUNE SYSTEM/RNA, IMMUNE SYSTEM-RNA complex; IMMUNE SYSTEM/RNA
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	— Å
rg_electron	107.20 Å
i0	19428800000.00
molecular_weight	1138900.0 kDa
excluded_volume	1405300 Å³
envelope_volume	2605500 Å³
shell_volume	225420 Å³
envelope_diameter	381.7 Å
shell_rg	83.91 Å
envelope_rg	102.90 Å
shape_rg	107.20 Å
total_rg	106.90 Å
total_atoms	155526
n_residues	10017
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	299.7 Å
rg_real	99.96 Å
rg_real_error	1.72 Å
i0_real	1.8780e+10
i0_real_error	4.4990e+08
rg_reciprocal	95.17 Å
i0_reciprocal	18810000000.0000
total_estimate	0.8872
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	85.6 Å
skewness	0.524
kurtosis	-0.528
angular_range	— – 0.0700 Å⁻¹
current_alpha	0.3676
highest_alpha	7208000000.0000
n_real_points	15
gnom_version	4.1.3
quality_criteria	AN1: 0.003; Oscil: 0.841; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.028

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	CRISPR-associated protein Csy3
formula_weight	36948.5 kDa
src_method	man
entity_count	30

Polymer

type	polypeptide(L)
strand_id	A,C,D,E,F,G,I,J,K,L,B,H,N,O,P,Q,S,T,U,V,W,Y,Z,a,b,f,i,o,p,q
atom_count	155526

MAKAATTLKTASVLAFERKLANSDALMYAGNWAQQDNWTAIAIQEKSVRGTISNRLKNALTSDPAKLDAEIQKANLQKVDVAALPFGADTLKIVFTLRVLGNLAQPSVCNDQDYQTALGDIITGYAQEQGFSTLAARYAENIANGRFLWRNRVGAEAIRVVVTKKGERSWEFNGEDYSLRQFSQPAGDLAALTQAIEKGLAGDASALFTVEAYVQLGNGQEVFPSQELVLDEKARNGKSKILYQVNDVAAIHSQKIGNALRTIDDWYPAADEAGPIAVEPYGSVTSRGKAYRQPREKMDFYTLLDNWVIKGDVPMPEQQHYVIATLIRGGVFGEKGE

Source

organism	Pectobacterium atrosepticum SCRI1043
common_name	Erwinia carotovora subsp. atroseptica
ncbi_taxonomy_id	218491
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	RNA (185-MER)
formula_weight	59971.7 kDa
src_method	man
entity_count	1

Polymer

type	polyribonucleotide
strand_id	M

CGGGAUUCACGGCGGGCUUGAAAUUCACGGCGAAAGCGGGCUUGAAAUUCACGGCGAAAUUCACGGCGGGCUUGAAAUUCACGGCGGGAUUCACGGCGGGCUUGAAAUUCACGGCGAAAUUCACGGCGGGCUUGAAAUUCACGGCGAAAUUCACGGCGGGCUUGAAAUUCACGGCGGGAUUCACG

Source

organism	Thiocystis violascens
ncbi_taxonomy_id	73141
host_organism	Escherichia coli BL21(DE3)

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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	4.58 Å
resolution_method	—
num_particles	168817

fit	/app/data/saxs_computation/xc/9xcf/9xcf.fit
pddf	/app/data/pr_computation/xc/9xcf/9xcf.pr.out
profile	/app/data/saxs_computation/xc/9xcf/9xcf.dat

Cryo-EM structure of csy3 with crRNA

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

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)