9vp8
Crystal structure of YdjB from Salmonella enterica subsp. enterica serovar Typhi
SAXS Profile
P(r) Distribution
1. Structure Basics
| entry_id | 9vp8 |
| deposition_date | 2025-07-02 |
| last_revision | 2025-10-22 |
| title | Crystal structure of YdjB from Salmonella enterica subsp. enterica serovar Typhi |
| keywords | YdjB-like protein, Nicotinamidase, aspartokinase, DE NOVO PROTEIN; DE NOVO PROTEIN |
| method | X-RAY DIFFRACTION |
Download Data
2. SAXS Parameters (CRYSOL)
| rg_guinier | 16.75 Å |
| rg_electron | 15.71 Å |
| i0 | 3639560.00 |
| molecular_weight | 13928.0 kDa |
| excluded_volume | 17680 ų |
| envelope_volume | 20847 ų |
| shell_volume | 11826 ų |
| envelope_diameter | 52.0 Å |
| shell_rg | 20.53 Å |
| envelope_rg | 15.90 Å |
| shape_rg | 15.67 Å |
| total_rg | 16.81 Å |
| total_atoms | 979 |
| n_residues | 129 |
| n_harmonics | 20 |
| q_range | — – 0.5000 Å−1 |
| n_points | 101 |
| shell_type | directional |
| solvent_density | 0.3340 e/ų |
| contrast_shell | 0.0300 e/ų |
| crysol_version | 4.1.3 |
3. P(r) Analysis (GNOM)
| dmax | 53.3 Å |
| rg_real | 16.72 Å |
| rg_real_error | 0.35 Å |
| i0_real | 3.6400e+06 |
| i0_real_error | 4.5870e+04 |
| rg_reciprocal | 16.73 Å |
| i0_reciprocal | 3640000.0000 |
| total_estimate | 0.8899 |
| solution_quality | GOOD a GOOD solution |
| n_peaks | 1 |
| r_peak_primary | 52.6 Å |
| skewness | 0.256 |
| kurtosis | -0.488 |
| angular_range | — – 0.4750 Å−1 |
| current_alpha | 0.0000 |
| highest_alpha | 627300.0000 |
| n_real_points | 78 |
| gnom_version | 4.1.3 |
| quality_criteria | AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.957 |