;Crystal structure of antibody Fab G001-58 from IAVI G001 human trial in complex with a germline-targeting gp120 engineered outer domain eOD-GT8-mingly ;

条目编号 entry_id	9oap
沉积日期 deposition_date	2025-04-21
最后修订 last_revision	2025-06-25
结构标题 title	;Crystal structure of antibody Fab G001-58 from IAVI G001 human trial in complex with a germline-targeting gp120 engineered outer domain eOD-GT8-mingly ;
关键词 keywords	HIV-1 Envelope antibody, HIV CD4 binding site antibody, IAVI G001 clinical trial, Germline-targeting immunogen, IMMUNE SYSTEM; IMMUNE SYSTEM
实验方法 method	X-RAY DIFFRACTION

回转半径 Rg (Guinier) rg_guinier	30.93 Å
回转半径 Rg (电子) rg_electron	30.71 Å
零角强度 I(0) i0	69159500.00
分子量 molecular_weight	64490.0 kDa
排除体积 excluded_volume	80252 ų
包络体积 envelope_volume	105020 ų
水化壳体积 shell_volume	30526 ų
包络直径 envelope_diameter	106.1 Å
壳层 Rg shell_rg	35.50 Å
包络 Rg envelope_rg	30.39 Å
形状 Rg shape_rg	30.65 Å
总 Rg total_rg	31.31 Å
总原子数 total_atoms	4541
残基数 n_residues	584
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/ų
壳层衬度 contrast_shell	0.0300 e/ų
CRYSOL 版本 crysol_version	4.1.3

最大尺寸 Dmax dmax	105.1 Å
Rg (实空间) rg_real	31.18 Å
Rg 误差 (实空间) rg_real_error	0.80 Å
I(0) (实空间) i0_real	6.9160e+07
I(0) 误差 (实空间) i0_real_error	1.0260e+06
Rg (倒空间) rg_reciprocal	31.08 Å
I(0) (倒空间) i0_reciprocal	69150000.0000
解质量估计 total_estimate	0.8472
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	28.9 Å
偏度 Skewness skewness	0.504
峰度 Kurtosis kurtosis	-0.361
角度范围 angular_range	— – 0.2550 Å−1
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	13430000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.807; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.745; Smooth: 0.842

晶胞参数 Unit Cell

晶胞边长 a length_a	110.080 Å
晶胞边长 b length_b	174.910 Å
晶胞边长 c length_c	93.581 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	8

对称性 Symmetry

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	orthorhombic

精修参数 Refinement

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	47.440 Å
R 因子 r_factor	0.2150
R_work r_work	0.2132
R_free r_free	0.2494

衍射实验 Diffraction

实验温度 temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/oa/9oap/pr_distribution.json
• pr_output /app/data/pr_computation/oa/9oap/9oap.pr.out
• pr_plot /app/data/visualization/pr_computation/oa/9oap/9oap_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/oa/9oap/9oap.dat
• saxs_fit /app/data/saxs_computation/oa/9oap/9oap.fit
• saxs_log /app/data/saxs_computation/oa/9oap/9oap.log
• saxs_plot /app/data/visualization/saxs_computation/oa/9oap/9oap_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/oa/9oap/9oap.fit
pddf	/app/data/pr_computation/oa/9oap/9oap.pr.out
profile	/app/data/saxs_computation/oa/9oap/9oap.dat