8f4d

RT XFEL structure of Photosystem II 50 microseconds after the third illumination at 2.15 Angstrom resolution

Method: X-RAY DIFFRACTION Dmax: 196.6 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

SAXS profile for 8f4d

P(r) 距离分布 P(r) Distribution

P(r) distribution for 8f4d
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1. 结构基本信息 1. Structure Basics

条目编号 entry_id8f4d
沉积日期 deposition_date2022-11-10
结构标题 titleRT XFEL structure of Photosystem II 50 microseconds after the third illumination at 2.15 Angstrom resolution
关键词 keywordswater oxidation, OEC, Manganese cluster, PHOTOSYNTHESIS; PHOTOSYNTHESIS
实验方法 methodX-RAY DIFFRACTION

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier57.83
回转半径 Rg (电子) rg_electron57.17
零角强度 I(0) i04667820000.00
分子量 molecular_weight706580.0 kDa
排除体积 excluded_volume933550 ų
包络体积 envelope_volume1094600 ų
水化壳体积 shell_volume150180 ų
包络直径 envelope_diameter210.7
壳层 Rg shell_rg64.80
包络 Rg envelope_rg57.42
形状 Rg shape_rg57.16
总 Rg total_rg57.42
总原子数 total_atoms50144
残基数 n_residues5302
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 −1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax196.6
Rg (实空间) rg_real57.75
Rg 误差 (实空间) rg_real_error1.46
I(0) (实空间) i0_real4.6680e+09
I(0) 误差 (实空间) i0_real_error9.6770e+07
Rg (倒空间) rg_reciprocal57.88
I(0) (倒空间) i0_reciprocal4669000000.0000
解质量估计 total_estimate0.8651
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary65.5
偏度 Skewness skewness0.330
峰度 Kurtosis kurtosis-0.337
角度范围 angular_range— – 0.1350 −1
当前正则化参数 α current_alpha0.0001
最高正则化参数 α highest_alpha643500000.0000
实空间数据点数 n_real_points28
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.813; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.804

4. 晶体学与实验 4. Crystallography & Experiment

5. 实体与聚合体信息 (37)

6. 折叠分类 (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

结构域编号 domain_id8f4dA01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology85 — Photosynthetic Reaction Center, subunit M; domain 1
同源超家族 H-superfamily homologous superfamily10 — Photosystem II protein D1-like
结构域编号 domain_id8f4dB01
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology680 — Photosystem II CP47 reaction center protein
同源超家族 H-superfamily homologous superfamily10 — Photosystem II CP47 reaction center protein
结构域编号 domain_id8f4dE01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily860 — Photosystem II cytochrome b559, alpha subunit
结构域编号 domain_id8f4dZ01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily740 — Photosystem II PsbZ, reaction centre
结构域编号 domain_id8f4da01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology85 — Photosynthetic Reaction Center, subunit M; domain 1
同源超家族 H-superfamily homologous superfamily10 — Photosystem II protein D1-like
结构域编号 domain_id8f4db01
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology680 — Photosystem II CP47 reaction center protein
同源超家族 H-superfamily homologous superfamily10 — Photosystem II CP47 reaction center protein
结构域编号 domain_id8f4de01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily860 — Photosystem II cytochrome b559, alpha subunit
结构域编号 domain_id8f4dz01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily740 — Photosystem II PsbZ, reaction centre

7. 引用文献 (1)

8. 文件与曲线 (10)