Crystal structure of the HIV V2-apex-targeting antibody RM038, derived from macaque ApexGT6 immunization

条目编号 entry_id	9mpb
沉积日期 deposition_date	2024-12-30
结构标题 title	Crystal structure of the HIV V2-apex-targeting antibody RM038, derived from macaque ApexGT6 immunization
关键词 keywords	HIV-1, Germline-targeting vaccination, ApexGT6, V2-apex antibody, IMMUNE SYSTEM; IMMUNE SYSTEM
实验方法 method	X-RAY DIFFRACTION

回转半径 Rg (Guinier) rg_guinier	25.59 Å
回转半径 Rg (电子) rg_electron	24.63 Å
零角强度 I(0) i0	40244400.00
分子量 molecular_weight	48065.0 kDa
排除体积 excluded_volume	59678 ų
包络体积 envelope_volume	74070 ų
水化壳体积 shell_volume	25421 ų
包络直径 envelope_diameter	94.5 Å
壳层 Rg shell_rg	31.36 Å
包络 Rg envelope_rg	24.59 Å
形状 Rg shape_rg	24.62 Å
总 Rg total_rg	25.43 Å
总原子数 total_atoms	5209
残基数 n_residues	421
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	91.4 Å
Rg (实空间) rg_real	25.60 Å
Rg 误差 (实空间) rg_real_error	0.85 Å
I(0) (实空间) i0_real	4.0240e+07
I(0) 误差 (实空间) i0_real_error	6.5220e+05
Rg (倒空间) rg_reciprocal	25.60 Å
I(0) (倒空间) i0_reciprocal	40240000.0000
解质量估计 total_estimate	0.7033
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	29.5 Å
偏度 Skewness skewness	0.369
峰度 Kurtosis kurtosis	-0.245
角度范围 angular_range	— – 0.3100 Å−1
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	8516000.0000
实空间数据点数 n_real_points	63
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.767; Stabil: 1.000; Sysdev: 0.315; Positv: 1.000; Valcen: 0.935; Smooth: 0.959

晶胞参数 Unit Cell

晶胞边长 a length_a	181.251 Å
晶胞边长 b length_b	66.512 Å
晶胞边长 c length_c	53.405 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	103.18 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

对称性 Symmetry

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	monoclinic

精修参数 Refinement

分辨率 resolution	1.980 Å
最低分辨率 resolution_low	41.580 Å
R 因子 r_factor	0.1873
R_work r_work	0.1855
R_free r_free	0.2211

衍射实验 Diffraction

实验温度 temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/mp/9mpb/pr_distribution.json
• pr_output /app/data/pr_computation/mp/9mpb/9mpb.pr.out
• pr_plot /app/data/visualization/pr_computation/mp/9mpb/9mpb_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/mp/9mpb/9mpb.dat
• saxs_fit /app/data/saxs_computation/mp/9mpb/9mpb.fit
• saxs_log /app/data/saxs_computation/mp/9mpb/9mpb.log
• saxs_plot /app/data/visualization/saxs_computation/mp/9mpb/9mpb_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/mp/9mpb/9mpb.fit
pddf	/app/data/pr_computation/mp/9mpb/9mpb.pr.out
profile	/app/data/saxs_computation/mp/9mpb/9mpb.dat