Crystal structure of an agonist bound GPCR
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 5ZTY | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | LIPIDIC CUBIC PHASE | | 293 | 100 mM HEPES sodium pH 7.0, 25% PEG 400, 220 mM Sodium sulfate decahydrate |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 3.31 | 67.19 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 33.96 | α = 90 |
| b = 140.22 | β = 90 |
| c = 156.26 | 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 | | 2018-10-19 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 1 | 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 | 3.2 | 44.78 | 87.6 | 0.171 | 0.2 | 0.986 | 4.26 | 2.847 | | 11476 | | | 96.93 |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 3.2 | 3.28 | 90.4 | | 0.673 | 0.789 | 0.627 | 1.22 | 2.796 | |
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 | 5zty | 3.2 | 44.78 | 11475 | 531 | 87.7 | 0.231 | 0.23 | 0.25 | 0.262 | 0.29 | RANDOM | 118.21 |
| 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] |
|---|
| 20.7169 | | | -22.8308 | | 2.1138 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| t_other_torsion | 19.89 |
| t_omega_torsion | 1.95 |
| t_angle_deg | 1.03 |
| t_bond_d | 0.009 |
| t_dihedral_angle_d | |
| t_trig_c_planes | |
| t_gen_planes | |
| t_it | |
| t_nbd | |
| t_improper_torsion | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| t_other_torsion | 19.89 |
| t_omega_torsion | 1.95 |
| t_angle_deg | 1.03 |
| t_bond_d | 0.009 |
| t_dihedral_angle_d | |
| t_trig_c_planes | |
| t_gen_planes | |
| t_it | |
| t_nbd | |
| t_improper_torsion | |
| t_pseud_angle | |
| 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 | 3471 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | 29 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| BUSTER | refinement |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| PHASER | phasing |
