SAXSdb — 22fn

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	22fn
沉积日期 deposition_date	2026-01-08
结构标题 title	Cryo-EM structure of AsCas12a in complex with crDNA and RNA target
关键词 keywords	Cas12a, crDNA, RNA, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	37.48 Å
回转半径 Rg (电子) rg_electron	37.49 Å
零角强度 I(0) i0	430853000.00
分子量 molecular_weight	158330.0 kDa
排除体积 excluded_volume	193700 Å³
包络体积 envelope_volume	269490 Å³
水化壳体积 shell_volume	59277 Å³
包络直径 envelope_diameter	123.7 Å
壳层 Rg shell_rg	44.15 Å
包络 Rg envelope_rg	36.78 Å
形状 Rg shape_rg	37.51 Å
总 Rg total_rg	37.83 Å
总原子数 total_atoms	11105
残基数 n_residues	1266
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	121.8 Å
Rg (实空间) rg_real	37.37 Å
Rg 误差 (实空间) rg_real_error	0.99 Å
I(0) (实空间) i0_real	4.3090e+08
I(0) 误差 (实空间) i0_real_error	7.8070e+06
Rg (倒空间) rg_reciprocal	37.44 Å
I(0) (倒空间) i0_reciprocal	430900000.0000
解质量估计 total_estimate	0.8939
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	46.4 Å
偏度 Skewness skewness	0.239
峰度 Kurtosis kurtosis	-0.439
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	92240000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.918

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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(PGPAPCPAPGPCPCPCPAPCPAPUPGPGPCPAPUPUPCPCPAPCP*U)-3') ;
分子量 formula_weight	14179.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	B
原子数 atom_count	11105

GACAGCCCACAUGGCAUUCCACUUAUCACUGGCAUCCUUCCACUC

Entity 2 polymer

描述 description	CRISPR-associated endonuclease Cas12a
分子量 formula_weight	151410.9 kDa
EC 编号 ec_number	3.1.21.1,4.6.1.22
突变 mutation	M537R/F870L
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

MTQFEGFTNLYQVSKTLRFELIPQGKTLKHIQEQGFIEEDKARNDHYKELKPIIDRIYKTYADQCLQLVQLDWENLSAAIDSYRKEKTEETRNALIEEQATYRNAIHDYFIGRTDNLTDAINKRHAEIYKGLFKAELFNGKVLKQLGTVTTTEHENALLRSFDKFTTYFSGFYENRKNVFSAEDISTAIPHRIVQDNFPKFKENCHIFTRLITAVPSLREHFENVKKAIGIFVSTSIEEVFSFPFYNQLLTQTQIDLYNQLLGGISREAGTEKIKGLNEVLNLAIQKNDETAHIIASLPHRFIPLFKQILSDRNTLSFILEEFKSDEEVIQSFCKYKTLLRNENVLETAEALFNELNSIDLTHIFISHKKLETISSALCDHWDTLRNALYERRISELTGKITKSAKEKVQRSLKHEDINLQEIISAAGKELSEAFKQKTSEILSHAHAALDQPLPTTLKKQEEKEILKSQLDSLLGLYHLLDWFAVDESNEVDPEFSARLTGIKLEMEPSLSFYNKARNYATKKPYSVEKFKLNFQRPTLASGWDVNKEKNNGAILFVKNGLYYLGIMPKQKGRYKALSFEPTEKTSEGFDKMYYDYFPDAAKMIPKCSTQLKAVTAHFQTHTTPILLSNNFIEPLEITKEIYDLNNPEKEPKKFQTAYAKKTGDQKGYREALCKWIDFTRDFLSKYTKTTSIDLSSLRPSSQYKDLGEYYAELNPLLYHISFQRIAEKEIMDAVETGKLYLFQIYNKDFAKGHHGKPNLHTLYWTGLFSPENLAKTSIKLNGQAELFYRPKSRMKRMAHRLGEKMLNKKLKDQKTPIPDTLYQELYDYVNHRLSHDLSDEARALLPNVITKEVSHEIIKDRRFTSDKFLFHVPITLNYQAANSPSKFNQRVNAYLKEHPETPIIGIDRGERNLIYITVIDSTGKILEQRSLNTIQQFDYQKKLDNREKERVAARQAWSVVGTIKDLKQGYLSQVIHEIVDLMIHYQAVVVLENLNFGFKSKRTGIAEKAVYQQFEKMLIDKLNCLVLKDYPAEKVGGVLNPYQLTDQFTSFAKMGTQSGFLFYVPAPYTSKIDPLTGFVDPFVWKTIKNHESRKHFLEGFDFLHYDVKTGDFILHFKMNRNLSFQRGLPGFMPAWDIVFEKNETQFDAKGTPFIAGKRIVPVIENHRFTGRYRDLYPANELIALLEEKGIVFRDGSNILPKLLENDDSHAIDTMVALIRSVLQMRNSNAATGEDYINSPVRDLNGVCFDSRFQNPEWPMDADANGAYHIALKGQLLLNHLKESKDLKLQNGISNQDWLAYIQELRN

来源 Source

来源生物 organism	Acidaminococcus sp. BV3L6
NCBI 分类编号 ncbi_taxonomy_id	1111120
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 3 polymer

描述 description	DNA (41-MER)
分子量 formula_weight	13352.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	C

AAGTGGAATGCCATGTGGGCTTAAAGGTGAATCCTTTATTAAT

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7. 引用文献 (1)

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分辨率 resolution	3.170 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

分辨率 resolution	3.17 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	54033

fit	/app/data/saxs_computation/2f/22fn/22fn.fit
pddf	/app/data/pr_computation/2f/22fn/22fn.pr.out
profile	/app/data/saxs_computation/2f/22fn/22fn.dat

Cryo-EM structure of AsCas12a in complex with crDNA and RNA target

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

精修参数 Refinement

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

来源 Source

Entity 3 polymer

聚合体 Polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)