SAXSdb — 9ua2

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1. Structure Basics

entry_id	9ua2
deposition_date	2025-03-31
title	Cryo-EM structure of PsCas9-sgRNA-dsDNA (30 nt) ternary complex
keywords	CRISPR-Cas9, RNA, DNA, complex, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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	40.30 Å
rg_electron	40.11 Å
i0	799983000.00
molecular_weight	202980.0 kDa
excluded_volume	242000 Å³
envelope_volume	342900 Å³
shell_volume	69739 Å³
envelope_diameter	136.9 Å
shell_rg	47.11 Å
envelope_rg	39.35 Å
shape_rg	40.10 Å
total_rg	40.47 Å
total_atoms	14114
n_residues	1535
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	130.0 Å
rg_real	40.24 Å
rg_real_error	0.92 Å
i0_real	8.0000e+08
i0_real_error	1.4920e+07
rg_reciprocal	40.30 Å
i0_reciprocal	800000000.0000
total_estimate	0.8807
solution_quality	GOOD a GOOD solution
n_peaks	0
r_peak_primary	— Å
skewness	0.306
kurtosis	-0.287
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	54560000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.741

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	CRISPR-associated endonuclease Cas9
formula_weight	165168.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	14114

HHHHHHVAGAGAGENLYFQGMTVKSTLAVDMGGRYTGIFSYTTDSGFPKAKEARAYVLNMPDNDALTYSMAARTQTRHRIRSQQRFVLARRLTYILIEGKLKRKLSPREKEAISSLLRRRGYSRLESELDLSVLQGVESGFFKCFLPNFDEDENLLTQWTSLTDGYLQNNSDSRRQIQIFLESSKDSKEFLTVVKSQHQDTKEYKNALKVMRDDAESMIEQSMFGHKHRRLYLEAIAQDIPRDSRLKPIIEAFSGVEKFHHFIGNLSNLQLRALRWYFNDPSMKNNVFDKERLKSVLVRAYQFFHYPKDLTQQRAEVLNAYEGATDILETLQTLNPELTIPPYEDQNNRRPPLDQTLWLSPRLLDQRYGDTWEIWVQNLLRSPLSKGIDENLDTILITTDRKARLLERQSGRLIHYTSQKLYHSYVLQRLLDRTVENDAYLLKTLVSSNRGNSNEIHQAQERLTRDLGSQHIKKFLDFVRQYYDEVDKAKRGLWFIVEKPLMERADIHPPMKNDSVILRLVGNILCVSDLVDLSFWTRKVKGQSTVRSLCTAIEKTRKEYGNSFNYLYQRALYLQSKGKKLSAEDKDFIKLQSNVLLVSDVIAEALDIKEEQKKKFANPFSLAQLYNIIETEKSGFISTTLAAVDENAWRNNLQGKARCVQLCADTVRPFDGALRNILDRQAYEIAKLKAEELLSTELKNQTIDLVVLLESNQFAFSASLAEVKKSANTAAIRQKVAKAQKRQQDRWLSKDERIKSASRGLCPYTGKNLGDKGEVDHIIPRSLSMNYMGSILNSEANLIYCSQEGAQLKLNGRKKLSDLADNYLKVVFGTADRGTICKYIEKSVSELTDAKIVQFELLDRSQQDAVRHALFLEDFSEARRRIIRLLGKINTARVNGTQAWFAKSFITKLRELTKEWCANNQITLAFDLYRLDAQTVSQDYRKKFALINKDWAKPDDKKQPIASHAIDAFCVFAAAKDKRNIANVLGVFDEVAEEQNLKTIAQLMPSEVNLISPKRKSILDKNEVGSRALMKEGIFAEHFLPILVRGDDCRIGFDWSESGSVKVKDADKLFGVLDGLLKQSQKRSVNGFETYTVDRIKAFELLHDVFIRPCSQKMLEQAEVLEKLHYITQNISVTSVYDAVNRQFKCREEILKDKDFDIKVDLGNRFGSAKGKITLPAKREWEKLVNRSELKNLIKDKLSDKGSEKTPDGETLIYDIFRSIPVQKLSHKATRRVWSLPKIPSISSGVRIKRKDSNGNDIYQLYMLNDTKCKGFVVNEKGVIDWSSDLVADLYKQPTLTILNGRYLKADQYVRMDQWYEVDCGRDDVIVKMCPGTSGRRYIEITQSKKQFEDWTGYISGSFWNYPVTIKLSSQQIANFVKNSQMPLLGKPRSGQITVITLGNTLKYWYCVESKNSMMNEAYQKAYLVHFNQKRPAAT

Source

organism	Parasutterella secunda
ncbi_taxonomy_id	626947
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	RNA (131-MER)
formula_weight	42108.9 kDa
src_method	man
entity_count	1

Polymer

type	polyribonucleotide
strand_id	B

GUGGGGCCACUAGGGACAGGAUGUUUCAGUUAUUCGUGAAAACGAAUGAAGUCACUCUUAAAGUGAGCUGAAAUCACUAAAAAUUAAGAUUGAACCCGGCUACUGACUCUGUCAUCCGGGUUUACUUAUUU

Source

organism	Parasutterella secunda
ncbi_taxonomy_id	626947
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	DNA (30-MER)
formula_weight	9394.0 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	C

GTGGGGCCACTAGGGACAGGATTGGTGACA

Source

organism	Parasutterella secunda
ncbi_taxonomy_id	626947
host_organism	Escherichia coli BL21(DE3)

Entity 4 polymer

description	DNA (30-MER)
formula_weight	9055.8 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	D

TGTCACCAATCCTGTCCCTAGTGGCCCCAC

Source

organism	Parasutterella secunda
ncbi_taxonomy_id	626947
host_organism	Escherichia coli BL21(DE3)

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	4

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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	2.830 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.83 Å
resolution_method	—
num_particles	253507

fit	/app/data/saxs_computation/ua/9ua2/9ua2.fit
pddf	/app/data/pr_computation/ua/9ua2/9ua2.pr.out
profile	/app/data/saxs_computation/ua/9ua2/9ua2.dat

Cryo-EM structure of PsCas9-sgRNA-dsDNA (30 nt) ternary complex

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

Refinement

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)