5XEZ
Structure of the Full-length glucagon class B G protein-coupled receptor
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4L6R | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | LIPIDIC CUBIC PHASE | 293 | 100mM HEPES, pH7.0, 300mM potassium phosphate monobasic, 25% PEG500DME, 100mM gly-gly-glycine | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.76 | 73.47 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 72.61 | α = 90 |
| b = 245.33 | β = 90.01 |
| c = 96.15 | 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 | 293 | PIXEL | CS-PAD CXI-1 | 2016-08-20 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE CXI | 1.3 | SLAC LCLS | CXI |
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 | 3 | 50 | 100 | 4.8 | 198 | 67598 | |||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4L6R | 3 | 31.78 | 63632 | 3311 | 99.79 | 0.21123 | 0.20953 | 0.24327 | RANDOM | 78.21 | ||||||
| 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] | |
| -5.16 | -4.17 | -8.98 | 14.14 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 38.224 |
| r_dihedral_angle_3_deg | 20.494 |
| r_dihedral_angle_4_deg | 16.328 |
| r_dihedral_angle_1_deg | 6.63 |
| r_long_range_B_refined | 4.643 |
| r_long_range_B_other | 4.643 |
| r_mcangle_it | 2.766 |
| r_mcangle_other | 2.766 |
| r_scangle_other | 2.055 |
| r_mcbond_it | 1.537 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 14804 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | 264 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| CrystFEL | data reduction |
| CrystFEL | data scaling |
| PHASER | phasing |
