SAXSdb — 9w9d

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1. Structure Basics

entry_id	9w9d
deposition_date	2025-08-09
title	SuperFi Cas9 - 22nt sgRNA - DNA ternary complex
keywords	Complex, cas, SuperFi cas9, IMMUNE SYSTEM; IMMUNE SYSTEM
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	39.06 Å
rg_electron	38.89 Å
i0	581788000.00
molecular_weight	165670.0 kDa
excluded_volume	194190 Å³
envelope_volume	291390 Å³
shell_volume	60926 Å³
envelope_diameter	134.6 Å
shell_rg	46.14 Å
envelope_rg	38.03 Å
shape_rg	38.89 Å
total_rg	39.24 Å
total_atoms	11479
n_residues	1165
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	124.2 Å
rg_real	38.89 Å
rg_real_error	0.75 Å
i0_real	5.8180e+08
i0_real_error	9.8520e+06
rg_reciprocal	39.00 Å
i0_reciprocal	581900000.0000
total_estimate	0.9012
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	49.7 Å
skewness	0.184
kurtosis	-0.515
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	62530000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.914

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	CRISPR-associated endonuclease Cas9/Csn1
formula_weight	158502.4 kDa
ec_number	3.1.-.-
mutation	Y1010D, Y1013D, Y1016D, V1018D, R1019D, Q1027D, K1031D
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	11479

MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVDGDDKVDDDDKMIAKSEDEIGDATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGD

Source

organism	Streptococcus pyogenes serotype M1
ncbi_taxonomy_id	301447
host_organism	Escherichia coli

Entity 2 polymer

description	DNA (50-MER)
formula_weight	15438.9 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

AGCTATGAGTGGCCCCTGTGGAGAGAAGCCTGTCCTGGAAGCCAGCCCCA

Entity 3 polymer

description	DNA (50-MER)
formula_weight	15371.8 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	C

TGGGGCTGGCTTCCAGGACAGGCTTCTCTCCACAGGGGCCACTCATAGCT

Entity 4 polymer

description	RNA (102-MER)
formula_weight	32815.5 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	D

CAGGACAGGCUUCUCUCCACAGGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU

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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	4.400 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.40 Å
resolution_method	—
num_particles	43148

fit	/app/data/saxs_computation/w9/9w9d/9w9d.fit
pddf	/app/data/pr_computation/w9/9w9d/9w9d.pr.out
profile	/app/data/saxs_computation/w9/9w9d/9w9d.dat

SuperFi Cas9 - 22nt sgRNA - DNA 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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)