Crystal structure of human alpha2C adrenergic G protein-coupled receptor.
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 4S0V | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | LIPIDIC CUBIC PHASE | | 293 | sodium phosphate monobasic (0.1M), Hepes pH6.5-6.9 (0.1M), PEG400 24-35% |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.52 | 51.1 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 74.48 | α = 90 |
| b = 78.74 | β = 90 |
| c = 190.45 | 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 | 100 | PIXEL | DECTRIS EIGER X 16M | | 2018-04-13 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 1.000 | 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) | Rrim I (All) | 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 | 2.8 | 50 | 94.4 | 0.11 | 0.127 | 0.996 | 8.15 | 3.74 | | 26778 | | | 79.97 |
| 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 | 2.8 | 2.87 | 82.1 | | 0.721 | 0.604 | 1.74 | 3.23 | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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) | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4s0v | 2.8 | 47.04 | 26777 | 1302 | 94.4 | 0.216 | 0.213 | 0.23 | 0.262 | 0.28 | RANDOM | 65 |
| 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] |
|---|
| -6.353 | | | 2.8413 | | 3.5116 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| t_other_torsion | 20.17 |
| t_omega_torsion | 2.62 |
| t_angle_deg | 1.09 |
| t_bond_d | 0.009 |
| t_dihedral_angle_d | |
| t_incorr_chiral_ct | |
| t_pseud_angle | |
| t_trig_c_planes | |
| t_gen_planes | |
| t_it | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| t_other_torsion | 20.17 |
| t_omega_torsion | 2.62 |
| t_angle_deg | 1.09 |
| t_bond_d | 0.009 |
| t_dihedral_angle_d | |
| t_incorr_chiral_ct | |
| t_pseud_angle | |
| t_trig_c_planes | |
| t_gen_planes | |
| t_it | |
| t_nbd | |
| t_improper_torsion | |
| t_chiral_improper_torsion | |
| t_sum_occupancies | |
| t_utility_distance | |
| t_utility_angle | |
| t_utility_torsion | |
| t_ideal_dist_contact | |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 7370 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 2 |
| Heterogen Atoms | 243 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| BUSTER | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| PHASER | phasing |
