De novo structure of the binary mosquito larvicide BinAB at pH 10
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 5FOY | PDB ENTRY 5FOY |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | | 10 | | NATURALLY OCCURRING NANOCRYSTALS FORMED IN VIVO, pH 10 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 3.05 | 59.4 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 86.67 | α = 90 |
| b = 97.286 | β = 90 |
| c = 127.654 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 21 21 21 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 287 | PIXEL | PIXEL ARRAY DETECTOR CSPAD | MIRRORS | 2015-02-13 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE CXI | 1.459 | SLAC LCLS | CXI |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot |
|---|
| 1 | 2.3 | 43.3 | 99.9 | 0.973 | 8.3 | 88.8 | | 6542289 | | 3 | 44.61 |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 2.3 | 2.35 | 99.9 | | 0.341 | 5.3 | 19.2 | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 5FOY | 2.4 | 24.045 | 1.34 | 42816 | 2000 | 99.98 | 0.1667 | 0.1645 | 0.17 | 0.2112 | 0.21 | |
| Temperature Factor Modeling |
|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
|---|
| | | | | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| f_dihedral_angle_d | 11.317 |
| f_angle_d | 0.611 |
| f_chiral_restr | 0.025 |
| f_plane_restr | 0.003 |
| f_bond_d | 0.002 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 6315 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 718 |
| Heterogen Atoms | 1 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| cctbx.xfel | data reduction |
| cctbx.prime | data scaling |
| SHELXD | phasing |
| PHENIX | phasing |
| PHENIX | refinement |
