Room temperature XFEL Isopenicillin N synthase structure in complex with the Fe(IV)=O mimic VO and ACV.
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 1BLZ | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | BATCH MODE | 8.5 | 298 | 1.7 M Li2So4, 0.1 M TRIS pH8.5 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.14 | 42.92 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 41.79 | α = 90 |
| b = 75.564 | β = 90 |
| c = 101.724 | 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 | 298 | CCD | RAYONIX MX300-HS | | 2019-07-10 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | FREE ELECTRON LASER | SACLA BEAMLINE BL2 | 1.23997 | SACLA | BL2 |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | | injection |
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 | 1.54 | 34.41 | 99.98 | 0.936 | 0.239 | 32.942 | 35.2 | | 48446 | | | 20.66 |
| 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 | 1.54 | 1.566 | 99.92 | | 0.026 | 1.269 | 0.706 | 11.56 | |
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 | FREE R-VALUE | 1BLZ | 1.54 | 34.41 | 1.3259 | 47861 | 1974 | 98.6784 | 0.1978 | 0.1966 | 0.2264 | 29.4261 |
| 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 | 9.483413 |
| f_angle_d | 1.00168 |
| f_chiral_restr | 0.059667 |
| f_bond_d | 0.010258 |
| f_plane_restr | 0.007271 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 2583 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 195 |
| Heterogen Atoms | 31 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| cctbx.xfel | data reduction |
| PHASER | phasing |
| cxi.merge | data scaling |
