Crystal structures of the alpha2A adrenergic receptor in complex with an antagonist RSC.
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 2Y02 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | LIPIDIC CUBIC PHASE | | 293 | 0.1M Sodium citrate tribasic dihydrate pH 5.0, 290mM Ammonium chloride, 30% PEG400, 7% glycerol |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 4.25 | 71.06 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 71.17 | α = 90 |
| b = 71.79 | β = 90 |
| c = 284.31 | γ = 90 |
| Symmetry |
|---|
| Space Group | C 2 2 21 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 S 6M | | 2016-09-23 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 0.97 | SPring-8 | BL41XU |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | | fixed target |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.7 | 49.7 | 91.4 | 0.089 | 0.999 | 9.7 | 8.1 | | 18743 | | | |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 2.7 | 2.85 | 73.4 | | 0.487 | 0.46 | | 2.5 | |
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 | R-Free | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2Y02 | 2.7 | 47.385 | 1.34 | 18724 | 867 | 91.15 | 0.252 | 0.2511 | 0.2669 | |
| 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 | 15.642 |
| f_angle_d | 0.526 |
| f_chiral_restr | 0.039 |
| f_bond_d | 0.003 |
| f_plane_restr | 0.003 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 2900 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | 79 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
