XFEL structure of apo CTX-M-15 after mixing for 0.7 sec with ertapenem using a piezoelectric injector (PolyPico)
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 6QW8 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | | 292 | 2.0 M ammonium sulphate, 0.1 M Tris 8.0 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.13 | 42.28 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 44.932 | α = 90 |
| b = 45.613 | β = 90 |
| c = 117.668 | 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 | 303 | CCD | RAYONIX MX300-HS | | 2019-07-12 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | FREE ELECTRON LASER | SACLA BEAMLINE BL2 | 1.2406 | SACLA | BL2 |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | Acoustic droplet ejection on conveyor belt with mixing using a pizoelectric injector | injection |
| Measurement |
|---|
| Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
|---|
| 1 | 10 (fs) | | 1.4 | 10 (KeV) | |
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 | 1.55 | 58.83 | 100 | 0.949 | 0.237 | 36.063 | 114.15 | | 35926 | | | 21.29 |
| 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 | 1.55 | 1.58 | | | 0.103 | 1.163 | 0.86 | | |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6qw8 | 1.55 | 32.01 | 1.33 | 35838 | 1769 | 99.73 | 0.1803 | 0.1789 | 0.18 | 0.206 | 0.21 | 29.74 |
| 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 | 19.0187 |
| f_angle_d | 1.0277 |
| f_chiral_restr | 0.0558 |
| f_bond_d | 0.0097 |
| f_plane_restr | 0.0071 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1942 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 158 |
| Heterogen Atoms | 5 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| cctbx.xfel | data reduction |
| PHASER | phasing |
