Pseudomonas fluorescens G150T isocyanide hydratase at 298 K XFEL data, thioimidate intermediate
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 6NI4 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | BATCH MODE | 8.8 | 298 | 15.5% PEG 3350, 125 MM MGCL2, AND 62 MM TRIS-HCL PH 8.8 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.25 | 45.23 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 72.136 | α = 90 |
| b = 59.758 | β = 115.883 |
| c = 56.11 | γ = 90 |
| Symmetry |
|---|
| Space Group | C 1 2 1 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 298 | CCD | RAYONIX MX340-HS | | 2021-04-10 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE MFX | 1.033 | SLAC LCLS | MFX |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | coMESH | injection |
| Measurement |
|---|
| Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
|---|
| 1 | 40 (fs) | 30 | 9 | 12 (KeV) | |
| Data Reduction |
|---|
| Diffraction ID | Frames Indexed | Crystal Hits | Frames Indexed | Latices Merged |
|---|
| 1 | | 17590 | | |
| Injection |
|---|
| Diffraction ID | Description | Flow Rate | Injector Diameter | Injection Power | Injector Nozzle | Filter Size | Carrier Solvent |
|---|
| 1 | | 6 (µl/min) | undefined (µm) | HPLC | | | |
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 | 1.3 | 21.98 | 99.97 | 0.97 | 0.163 | 4.7 | 40.51 | | 52683 | | | 15.15 |
| 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 | 1.3 | 1.32 | 100 | | 0.527 | 0.636 | 1.3 | 16.85 | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | 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 | FOURIER SYNTHESIS | FREE R-VALUE | 1.3 | 21.98 | 1.34 | 52672 | 2000 | 99.98 | 0.1383 | 0.137 | 0.1713 | 20.25 |
| 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 | 11.7587 |
| f_angle_d | 0.7867 |
| f_chiral_restr | 0.0756 |
| f_plane_restr | 0.0071 |
| f_bond_d | 0.0052 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1673 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 154 |
| Heterogen Atoms | 12 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| cctbx.xfel | data reduction |
| cctbx.xfel.merge | data scaling |
| PHASER | phasing |
