Unspecific peroxygenase from Psathyrella aberdarensis (PabUPO-II) in complex with alpha-ionone
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5OXU | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 291 | 1.85M ammonium sulphate, 100 mM BisTris pH 6.5 Soaking: 20 mM alpha-ionone 7 hours, cryoprotected with 20% glycerol | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 4.29 | 71.36 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 270.969 | α = 90 |
| b = 75.05 | β = 112.06 |
| c = 106.056 | 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 | 100 | PIXEL | DECTRIS PILATUS 6M | KB MIRRORS | 2021-06-19 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ALBA BEAMLINE XALOC | 0.979 | ALBA | XALOC |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.2 | 49.19 | 98.5 | 0.116 | 0.13 | 0.056 | 0.995 | 10.5 | 5.2 | 508304 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 2.2 | 2.24 | 98 | 0.881 | 0.972 | 0.407 | 0.898 | 3.2 | 5.3 | ||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | 2.2 | 49.19 | 93809 | 4833 | 98.21 | 0.18395 | 0.18246 | 0.188 | 0.21267 | 0.2179 | RANDOM | 43.29 | |||||
| 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] | |
| -2.71 | 0.14 | 4.15 | -1.17 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_3_deg | 11.908 |
| r_long_range_B_other | 8.97 |
| r_long_range_B_refined | 8.948 |
| r_scangle_other | 7.521 |
| r_dihedral_angle_2_deg | 6.474 |
| r_dihedral_angle_1_deg | 6.427 |
| r_mcangle_other | 5.327 |
| r_mcangle_it | 5.326 |
| r_scbond_it | 4.969 |
| r_scbond_other | 4.938 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 8338 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 562 |
| Heterogen Atoms | 18 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| XDS | data scaling |
| REFMAC | phasing |
