9kj6

Crystal Structure of SpCas9 ternary complex, amino acids (1242-1263) replaced with Gly-Ser linker

Method: X-RAY DIFFRACTION D_max: 145.5 Å Quality: REASONABLE

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9kj6
沉积日期 deposition_date	2024-11-12
结构标题 title	Crystal Structure of SpCas9 ternary complex, amino acids (1242-1263) replaced with Gly-Ser linker
关键词 keywords	CRISPR-Cas9, DNA BINDING PROTEIN; DNA BINDING PROTEIN
实验方法 method	X-RAY DIFFRACTION

▼

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

回转半径 Rg (Guinier) rg_guinier	40.31 Å
回转半径 Rg (电子) rg_electron	39.47 Å
零角强度 I(0) i0	783433000.00
分子量 molecular_weight	188760.0 kDa
排除体积 excluded_volume	218930 Å³
包络体积 envelope_volume	331580 Å³
水化壳体积 shell_volume	68843 Å³
包络直径 envelope_diameter	157.8 Å
壳层 Rg shell_rg	46.19 Å
包络 Rg envelope_rg	39.12 Å
形状 Rg shape_rg	39.47 Å
总 Rg total_rg	39.80 Å
总原子数 total_atoms	13121
残基数 n_residues	1479
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

▼

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

最大尺寸 Dmax dmax	145.5 Å
Rg (实空间) rg_real	42.15 Å
Rg 误差 (实空间) rg_real_error	0.66 Å
I(0) (实空间) i0_real	7.8570e+08
I(0) 误差 (实空间) i0_real_error	1.1180e+07
Rg (倒空间) rg_reciprocal	40.31 Å
I(0) (倒空间) i0_reciprocal	783500000.0000
解质量估计 total_estimate	0.6596
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	48.5 Å
偏度 Skewness skewness	0.581
峰度 Kurtosis kurtosis	0.370
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	1.4830
最高正则化参数 α highest_alpha	70160000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.726; Stabil: 0.883; Sysdev: 0.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.794

▶

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

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	CRISPR-associated endonuclease Cas9/Csn1
分子量 formula_weight	156702.6 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	A
原子数 atom_count	13121

GAASMDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDAIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHGSGSGSGHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGD

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

Entity 2 polymer

描述 description	single-guide RNA
分子量 formula_weight	32991.6 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

GGUAAAAGGGCGAUCUAAUGAAGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU

Entity 3 polymer

描述 description	Target Strand of double-stranded DNA
分子量 formula_weight	13126.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	C

TTGATTCTTACAGCGGTCGACCATTCATTAGATCGCCCTTTTA

Entity 4 polymer

描述 description	Non-target Strand of double-stranded DNA
分子量 formula_weight	8349.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	D

TGAATGGTCGACCGCTGTAAGAATCAA

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	88.550 Å
晶胞边长 b length_b	146.850 Å
晶胞边长 c length_c	222.360 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	4

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	orthorhombic

分辨率 resolution	3.590 Å
最低分辨率 resolution_low	29.900 Å
R 因子 r_factor	0.2301
R_work r_work	0.2280
R_free r_free	0.2705

fit	/app/data/saxs_computation/kj/9kj6/9kj6.fit
pddf	/app/data/pr_computation/kj/9kj6/9kj6.pr.out
profile	/app/data/saxs_computation/kj/9kj6/9kj6.dat

Crystal Structure of SpCas9 ternary complex, amino acids (1242-1263) replaced with Gly-Ser linker

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

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合体信息 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)