9om3

;Two Component Protein Nano-Particle (T=3). De Novo Design, Computationally Relaxed into Low Resolution Single Particle CryoEM Map with Icosahedral Symmetry Applied ;

Method: ELECTRON MICROSCOPY D_max: 668.3 Å Quality: GOOD

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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9om3
沉积日期 deposition_date	2025-05-13
结构标题 title	;Two Component Protein Nano-Particle (T=3). De Novo Design, Computationally Relaxed into Low Resolution Single Particle CryoEM Map with Icosahedral Symmetry Applied ;
关键词 keywords	Goldberg icosahedron, C60, Fullerene, DE NOVO PROTEIN; DE NOVO 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	— Å
回转半径 Rg (电子) rg_electron	278.70 Å
零角强度 I(0) i0	814985000000.00
分子量 molecular_weight	7870500.0 kDa
排除体积 excluded_volume	9938500 Å³
包络体积 envelope_volume	45275000 Å³
水化壳体积 shell_volume	1434800 Å³
包络直径 envelope_diameter	688.5 Å
壳层 Rg shell_rg	286.80 Å
包络 Rg envelope_rg	224.70 Å
形状 Rg shape_rg	278.70 Å
总 Rg total_rg	278.60 Å
总原子数 total_atoms	553500
残基数 n_residues	71640
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	668.3 Å
Rg (实空间) rg_real	284.40 Å
Rg 误差 (实空间) rg_real_error	0.45 Å
I(0) (实空间) i0_real	8.7210e+11
I(0) 误差 (实空间) i0_real_error	1.9850e+10
Rg (倒空间) rg_reciprocal	169.10 Å
I(0) (倒空间) i0_reciprocal	286900000000.0000
解质量估计 total_estimate	0.8301
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	401.0 Å
偏度 Skewness skewness	-0.438
峰度 Kurtosis kurtosis	-0.892
角度范围 angular_range	— – 0.0250 Å⁻¹
当前正则化参数 α current_alpha	1.9080
最高正则化参数 α highest_alpha	91260000000.0000
实空间数据点数 n_real_points	6
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 11.400; Oscil: 0.998; Stabil: 0.928; Sysdev: 1.000; Positv: 1.000; Valcen: 0.000; Smooth: 0.021

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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 (2)

Entity 1 polymer

描述 description	C2-B
分子量 formula_weight	12591.4 kDa
来源方法 src_method	man
拷贝数 entity_count	180

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	;A,C,E,G,I,K,M,O,Q,S,U,W,Y,a,c,e,g,i,k,m,o,q,s,u,w,y,ZA,ZC,ZE,ZG,ZI,AA,AC,AE,AG,AI,AK,AM,AO,AQ,AS,AU,AW,AY,Aa,Ac,Ae,Ag,Ai,Ak,Am,Ao,Aq,As,Au,Aw,Ay,ZK,ZM,ZO,ZQ,ZS,BA,BC,BE,BG,BI,BK,BM,BO,BQ,BS,BU,BW,BY,Ba,Bc,Be,Bg,Bi,Bk,Bm,Bo,Bq,Bs,Bu,Bw,By,ZU,ZW,ZY,YA,YC,CA,CC,CE,CG,CI,CK,CM,CO,CQ,CS,CU,CW,CY,Ca,Cc,Ce,Cg,Ci,Ck,Cm,Co,Cq,Cs,Cu,Cw,Cy,YE,YG,YI,YK,YM,DA,DC,DE,DG,DI,DK,DM,DO,DQ,DS,DU,DW,DY,Da,Dc,De,Dg,Di,Dk,Dm,Do,Dq,Ds,Du,Dw,Dy,YO,YQ,YS,YU,YW,EA,EC,EE,EG,EI,EK,EM,EO,EQ,ES,EU,EW,EY,Ea,Ec,Ee,Eg,Ei,Ek,Em,Eo,Eq,Es,Eu,Ew ;
原子数 atom_count	553500

PTLRVEIEGPAADVAALLRGVAELAAERAPKLAPVVAVIADFVASRPGPVRVRVEMGDGVLRVVLEGLHIKQQRQLYRDVRETSKKQGVETEIEVEGDTVTIVVRELEHHHHHH

来源 Source

来源生物 organism	synthetic construct
NCBI 分类编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 polymer

描述 description	C3-A
分子量 formula_weight	33381.5 kDa
来源方法 src_method	man
拷贝数 entity_count	180

聚合体 Polymer

聚合体类型 type

polypeptide(L)

链编号 strand_id

;B,D,F,H,J,L,N,P,R,T,V,X,Z,b,d,f,h,j,l,n,p,r,t,v,x,z,ZB,ZD,ZF,ZH,ZJ,AB,AD,AF,AH,AJ,AL,AN,AP,AR,AT,AV,AX,AZ,Ab,Ad,Af,Ah,Aj,Al,An,Ap,Ar,At,Av,Ax,Az,ZL,ZN,ZP,ZR,ZT,BB,BD,BF,BH,BJ,BL,BN,BP,BR,BT,BV,BX,BZ,Bb,Bd,Bf,Bh,Bj,Bl,Bn,Bp,Br,Bt,Bv,Bx,Bz,ZV,ZX,ZZ,YB,YD,CB,CD,CF,CH,CJ,CL,CN,CP,CR,CT,CV,CX,CZ,Cb,Cd,Cf,Ch,Cj,Cl,Cn,Cp,Cr,Ct,Cv,Cx,Cz,YF,YH,YJ,YL,YN,DB,DD,DF,DH,DJ,DL,DN,DP,DR,DT,DV,DX,DZ,Db,Dd,Df,Dh,Dj,Dl,Dn,Dp,Dr,Dt,Dv,Dx,Dz,YP,YR,YT,YV,YX,EB,ED,EF,EH,EJ,EL,EN,EP,ER,ET,EV,EX,EZ,Eb,Ed,Ef,Eh,Ej,El,En,Ep,Er,Et,Ev,Ex ;

SDEAIKRLLEELRASTAELKRATASLRAITEELKKNPSEDALVEHNRAIVEHNAIIVENNRIIAAVLEAIVAEFILAKARLLVWEARKKGNPEEVLEAAKKALRVAEEAAKAGIEAIFKAAAEAALEIAMRLIDLATKKGDPDLVREAQKVAERVAELADKNGDEEVKLKAYAAAVAAEIIRRIETLKRSGSSYEDIRQTLRETLERIIEELKRRGVDSSQIVWAIIYVAVAVMGVTMETHKSGNEVKVVIKGLHESQQEELLELVLRAAELAGVRVRIRFKGDTVTIVVRGLEHHHHHH

来源 Source

来源生物 organism	synthetic construct
NCBI 分类编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

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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	triclinic

分辨率 resolution	17.45 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	11155

fit	/app/data/saxs_computation/om/9om3/9om3.fit
pddf	/app/data/pr_computation/om/9om3/9om3.pr.out
profile	/app/data/saxs_computation/om/9om3/9om3.dat

;Two Component Protein Nano-Particle (T=3). De Novo Design, Computationally Relaxed into Low Resolution Single Particle CryoEM Map with Icosahedral Symmetry Applied ;

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 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)