XFEL A2aR structure by ligand exchange from LUF5843 to ZM241385.
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 4EIY | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | LIPIDIC CUBIC PHASE | | 293 | 50mM sodium thiocyanate, 100 mM sodium citrate pH 4.8, and 28% PEG 400, 2 mM of target ligand ZM241385 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.62 | 53.13 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 40.32 | α = 90 |
| b = 180.49 | β = 90 |
| c = 142.48 | 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 | 293 | PIXEL | CS-PAD CXI-2 | | 2017-12-07 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE CXI | 1.33 | SLAC LCLS | CXI |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | | injection |
| Measurement |
|---|
| Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
|---|
| 1 | 30 (fs) | 120 | 1.5 | 9.83 (KeV) | |
| Data Reduction |
|---|
| Diffraction ID | Frames Indexed | Crystal Hits | Frames Indexed | Latices Merged |
|---|
| 1 | 39281 | 68623 | 39281 | |
| Injection |
|---|
| Diffraction ID | Description | Flow Rate | Injector Diameter | Injection Power | Injector Nozzle | Filter Size | Carrier Solvent |
|---|
| 1 | | 0.2 (µl/min) | undefined (µm) | | | | |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | R Split (All) | 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 | 1.85 | 33.5 | 100 | 0.983 | 0.136 | 4.6 | 118 | | 45163 | | | |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 1.85 | 1.9 | | | 0.159 | 2.17 | | | |
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 | THROUGHOUT | 4eiy | 1.85 | 33.494 | 1.34 | 45044 | 1233 | 99.94 | 0.1762 | 0.1755 | 0.2008 | 51.8642 |
| 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 | 16.583 |
| f_angle_d | 1.053 |
| f_chiral_restr | 0.058 |
| f_bond_d | 0.009 |
| f_plane_restr | 0.006 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 2987 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 105 |
| Heterogen Atoms | 419 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHASER | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| CrystFEL | data reduction |
| CrystFEL | data scaling |
