Reductive-half reaction intermediate of copper amine oxidase from Arthrobacter globiformis captured with long-a-axis diffraction data by mix-and-inject serial crystallography at 50-ms time delay
X-RAY DIFFRACTION
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3WA2 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | BATCH MODE | 289 | 1.05M potassium/sodium tartrate in 25mM HEPES buffer pH 7.4 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.22 | 61.83 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 193.66 | α = 90 |
| b = 64.9 | β = 116.97 |
| c = 158.61 | 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 | 299 | CCD | MPCCD | 2021-06-03 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | FREE ELECTRON LASER | SACLA BEAMLINE BL2 | 1.24 | 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) | 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 | 1.86 | 30 | 100 | 0.8936855 | 3.1 | 34.2 | 288926 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 1.86 | 1.93 | 0.5240452 | ||||||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.86 | 29.92 | 1.35 | 288783 | 14431 | 99.93 | 0.225 | 0.2231 | 0.2234 | 0.26 | 0.2596 | ||||||
| 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 | 6.535 |
| f_angle_d | 0.978 |
| f_chiral_restr | 0.063 |
| f_plane_restr | 0.01 |
| f_bond_d | 0.008 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 9738 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 949 |
| Heterogen Atoms | 2 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHENIX | refinement |
| CrystFEL | data scaling |
| PHASER | phasing |
| CrystFEL | data reduction |
