SAXSdb — 9w7v

▼

1. Structure Basics

entry_id	9w7v
deposition_date	2025-08-07
title	SuperFi Cas9 - 20nt sgRNA - DNA ternary complex Class D
keywords	Complex, cas, SuperFi cas9, IMMUNE SYSTEM; IMMUNE SYSTEM
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	39.40 Å
rg_electron	39.03 Å
i0	738852000.00
molecular_weight	193400.0 kDa
excluded_volume	230160 Å³
envelope_volume	343640 Å³
shell_volume	71304 Å³
envelope_diameter	138.6 Å
shell_rg	46.53 Å
envelope_rg	38.22 Å
shape_rg	39.03 Å
total_rg	39.41 Å
total_atoms	13453
n_residues	1432
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	130.9 Å
rg_real	39.17 Å
rg_real_error	0.87 Å
i0_real	7.3890e+08
i0_real_error	1.2800e+07
rg_reciprocal	39.31 Å
i0_reciprocal	739000000.0000
total_estimate	0.8819
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	49.1 Å
skewness	0.200
kurtosis	-0.380
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0001
highest_alpha	76610000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.985

▶

4. Crystallography & Experiment

▶

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	13453

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 (100-MER)
formula_weight	32181.1 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	D

GGACAGGCUUCUCUCCACAGGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU

▶

6. Citations (1)

▶

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	3.810 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.81 Å
resolution_method	—
num_particles	41913

fit	/app/data/saxs_computation/w7/9w7v/9w7v.fit
pddf	/app/data/pr_computation/w7/9w7v/9w7v.pr.out
profile	/app/data/saxs_computation/w7/9w7v/9w7v.dat

SuperFi Cas9 - 20nt sgRNA - DNA ternary complex Class D

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)