SAXSdb — 9b2k

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9b2k
沉积日期 deposition_date	2024-03-15
结构标题 title	SpCas9 with dual-guide RNA in open conformation
关键词 keywords	Cas9, RNA, HYDROLASE; HYDROLASE
实验方法 method	ELECTRON MICROSCOPY

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	41.10 Å
回转半径 Rg (电子) rg_electron	39.52 Å
零角强度 I(0) i0	399380000.00
分子量 molecular_weight	146700.0 kDa
排除体积 excluded_volume	177270 Å³
包络体积 envelope_volume	269860 Å³
水化壳体积 shell_volume	58045 Å³
包络直径 envelope_diameter	132.5 Å
壳层 Rg shell_rg	44.46 Å
包络 Rg envelope_rg	38.70 Å
形状 Rg shape_rg	39.44 Å
总 Rg total_rg	40.04 Å
总原子数 total_atoms	10242
残基数 n_residues	1136
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	134.8 Å
Rg (实空间) rg_real	41.14 Å
Rg 误差 (实空间) rg_real_error	1.10 Å
I(0) (实空间) i0_real	3.9940e+08
I(0) 误差 (实空间) i0_real_error	7.1930e+06
Rg (倒空间) rg_reciprocal	41.10 Å
I(0) (倒空间) i0_reciprocal	399400000.0000
解质量估计 total_estimate	0.8647
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	46.1 Å
偏度 Skewness skewness	0.365
峰度 Kurtosis kurtosis	-0.387
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	53880000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.529

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	;RNA (5'-R(PGPUPUPUPUPAPGPAPGPCPUPAPUPGPCPUPGPU)-3') ;
分子量 formula_weight	13370.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	A
原子数 atom_count	10242

UACCAGCAAAACACUCCGAUGUUUUAGAGCUAUGCUGUUUUG

Entity 2 polymer

描述 description	RNA (56-MER)
分子量 formula_weight	22574.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	B

AAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUU

Entity 3 polymer

描述 description	CRISPR-associated endonuclease Cas9/Csn1
分子量 formula_weight	160774.3 kDa
EC 编号 ec_number	3.1.-.-
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	P

MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGDPKKKRKVMDKHHHHHH

来源 Source

来源生物 organism	Streptococcus pyogenes
NCBI 分类编号 ncbi_taxonomy_id	1314
宿主生物 host_organism	Escherichia coli

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7. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	—

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	3.67 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	164524

fit	/app/data/saxs_computation/b2/9b2k/9b2k.fit
pddf	/app/data/pr_computation/b2/9b2k/9b2k.pr.out
profile	/app/data/saxs_computation/b2/9b2k/9b2k.dat

SpCas9 with dual-guide RNA in open conformation

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

冷冻电镜 EM 3D

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

来源 Source

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)