Crystal structure of NS1-ED of Vietnam influenza A virus in complex with the p85-beta-iSH2 domain of human PI3K
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6OX7 | PDB entry 6OX7 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | SMALL TUBES | 278 | 20 mM sodium phosphate, pH 7.0, 80 mM sodium chloride | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.86 | 57.06 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 61.44 | α = 90 |
| b = 92.84 | β = 105.03 |
| c = 67.12 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 120 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2021-01-15 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 | ||
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 | 3.1 | 64.82 | 99 | 0.975 | 4 | 3.52 | 13030 | 74.29 | |||||||||||
| 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 | 3.1 | 3.31 | 0.614 | ||||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation 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 | FREE R-VALUE | PDB entry 6OX7 | 3.1 | 50 | 1.36 | 13026 | 625 | 97.86 | 0.2444 | 0.2429 | 0.25 | 0.2762 | 0.28 | 81.95 | ||||
| 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 | 14.8653 |
| f_angle_d | 0.4469 |
| f_chiral_restr | 0.0363 |
| f_plane_restr | 0.0029 |
| f_bond_d | 0.002 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4204 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHENIX | refinement |
| PHENIX | refinement |
| MOSFLM | data reduction |
| HKL-2000 | data scaling |
| PHENIX | phasing |
