Crystal structure of the HIV V2-apex-targeting antibody RM018 from macaque

条目编号 entry_id	9mpc
沉积日期 deposition_date	2024-12-30
结构标题 title	Crystal structure of the HIV V2-apex-targeting antibody RM018 from macaque
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	26.23 Å
回转半径 Rg (电子) rg_electron	25.39 Å
零角强度 I(0) i0	37429400.00
分子量 molecular_weight	46907.0 kDa
排除体积 excluded_volume	58462 ų
包络体积 envelope_volume	73061 ų
水化壳体积 shell_volume	24702 ų
包络直径 envelope_diameter	94.5 Å
壳层 Rg shell_rg	31.73 Å
包络 Rg envelope_rg	25.25 Å
形状 Rg shape_rg	25.36 Å
总 Rg total_rg	26.17 Å
总原子数 total_atoms	3708
残基数 n_residues	411
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	91.2 Å
Rg (实空间) rg_real	26.29 Å
Rg 误差 (实空间) rg_real_error	0.98 Å
I(0) (实空间) i0_real	3.7430e+07
I(0) 误差 (实空间) i0_real_error	5.9620e+05
Rg (倒空间) rg_reciprocal	26.27 Å
I(0) (倒空间) i0_reciprocal	37430000.0000
解质量估计 total_estimate	0.8741
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	28.9 Å
偏度 Skewness skewness	0.394
峰度 Kurtosis kurtosis	-0.258
角度范围 angular_range	— – 0.3000 Å−1
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	5380000.0000
实空间数据点数 n_real_points	61
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.898; Smooth: 0.990

晶胞参数 Unit Cell

晶胞边长 a length_a	118.702 Å
晶胞边长 b length_b	118.702 Å
晶胞边长 c length_c	194.418 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	16

对称性 Symmetry

空间群 space_group	I 4 2 2
空间群编号 int_tables_number	97
晶系 crystal_system	—

精修参数 Refinement

分辨率 resolution	3.300 Å
最低分辨率 resolution_low	29.710 Å
R 因子 r_factor	0.2547
R_work r_work	0.2490
R_free r_free	0.3073

衍射实验 Diffraction

实验温度 temperature

100.0 K

Files (7)

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

Curves (3)

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