5SVK
Crystal structure of the ATP-gated human P2X3 ion channel in the ATP-bound, open state
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 277.15 | 20% PEG 400, 50 mM ADA, pH 6.5 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 5.36 | 77.04 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 173.15 | α = 90 |
| b = 173.15 | β = 90 |
| c = 173.15 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 3 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2015-10-11 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 1.0 | ALS | 5.0.2 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.77 | 50 | 99.2 | 12.34 | 3.94 | 79845 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.773 | 43.287 | 0.83 | 79821 | 4010 | 93.9 | 0.2019 | 0.2005 | 0.2277 | ||||||||
| 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 | 16.847 |
| f_angle_d | 0.892 |
| f_chiral_restr | 0.09 |
| f_plane_restr | 0.004 |
| f_bond_d | 0.003 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5503 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 61 |
| Heterogen Atoms | 273 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
