← Back to search

9udi

Cryo-EM structure of the RdCas12n-sgRNA-DNA ternary complex, Conformation 2

Method: ELECTRON MICROSCOPY D_max: 95.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9udi
deposition_date	2025-04-06
title	Cryo-EM structure of the RdCas12n-sgRNA-DNA ternary complex, Conformation 2
keywords	CRISPR-Cas, Complex, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA-RNA complex; DNA BINDING PROTEIN/DNA/RNA
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	30.25 Å
rg_electron	29.37 Å
i0	178599000.00
molecular_weight	73404.0 kDa
excluded_volume	77731 Å³
envelope_volume	121370 Å³
shell_volume	35294 Å³
envelope_diameter	101.8 Å
shell_rg	35.59 Å
envelope_rg	29.46 Å
shape_rg	29.32 Å
total_rg	29.91 Å
total_atoms	4986
n_residues	397
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	95.4 Å
rg_real	30.14 Å
rg_real_error	0.62 Å
i0_real	1.7860e+08
i0_real_error	2.7360e+06
rg_reciprocal	30.19 Å
i0_reciprocal	178600000.0000
total_estimate	0.9022
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	38.5 Å
skewness	0.211
kurtosis	-0.373
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	8124000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.945

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	Transposase
formula_weight	61318.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4986

MATTDKKDEENLRAYKFRLDPNQAQTTALYQAVGAARYTYNMLTAYNLEVNRLRDDYWKRRHDEDISDADIKKELNALAKEDKRYKQLNYGAFGTQYLTPEKKRHEQAEHRIENGEDPSVVWNQETERSANPWLHTANQRVLVSGLQNASDAWDNFWASRTGKRAGRLVGTPRFKKKGVSRDSFTVPAPEKMGAYGTAYLRGEPAYKQGRRKITDYRHVRLSYLGTIRTFNSTKPLVKAVVAGAKIRSYTVSRNADRWYVSFLVKFSEPIRRSATKRARAAGSVGVDLGVKYLASLSDSEAPQRFPNLKFVEGLPSLENPRWSEASSRRLHKLQRALARSQKGSNRRSRLVKQIARLHHMTALRRESNLHQLTKKLATEYTLVGFEDLNVSGMTASAKGTVENPGKNVAQKSGLNRVVLDAAFGVFRNQLEYKAVWYGSAFEKVDRYFASSQTCSECGRKAKTKLTLRDRVFDCAYCGNMMDRDLNAAVNICREAQRLFDEKLASEDRESLNGRGSRGALRGAETVEASRPPASHRRGSP

Source

organism	Rothia dentocariosa
ncbi_taxonomy_id	2047
host_organism	Escherichia coli

Entity 2 polymer

description	DNA (40-MER)
formula_weight	12205.8 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	C

GGCAGTGTTTTCACTTTCACCTGAACCGGTTTCTCACAGC

Entity 3 polymer

description	;DNA (5'-D(PGPCPTPGPTPGPAPGPAPAPAPCPCPG)-3') ;
formula_weight	4329.8 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	D

GCTGTGAGAAACCG

Entity 4 polymer

description	sgRNA
formula_weight	69274.1 kDa
src_method	man
entity_count	1

Polymer

type	polyribonucleotide
strand_id	R

CUUUUUGACGAAAAACUCGCCUCAGAAGAUAGGGAGAGUCUAAACGGACGUGGAAGUCGAGGCGCUCUUCGGGGUGCUGAGACUGUGGAAGCGUCAAGACCACCUGCGAGUCAUCGUAGAGGGUCACCGUAGAUGAGUAAUCAUCUGCCCAUCUAUUGCAUUAUGCACGCGAAAGCGUGUGCAUGGGUGGUUCCCGGUUCAGGUGAAAGUGAAA

Source

organism	Rothia dentocariosa
ncbi_taxonomy_id	2047
host_organism	Escherichia coli

▶

6. Citations (1)

▶

resolution	3.01 Å
resolution_method	—
num_particles	879820

fit	/app/data/saxs_computation/ud/9udi/9udi.fit
pddf	/app/data/pr_computation/ud/9udi/9udi.pr.out
profile	/app/data/saxs_computation/ud/9udi/9udi.dat

Cryo-EM structure of the RdCas12n-sgRNA-DNA ternary complex, Conformation 2

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)