Dye type peroxidase Aa from Streptomyces lividans: 78.4 kGy structure
Serial Crystallography (SX)
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | BATCH MODE | 8 | 293 | 7 mg/ml protein mixed with 17% PEG 1500 and 67 mM MIB buffer (comprising imidazole, malonate and boric acid) |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.28 | 46.16 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 73.01 | α = 90 |
| b = 68.362 | β = 105.67 |
| c = 74.937 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 1 21 1 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 293 | PIXEL | DECTRIS PILATUS3 6M | | 2017-06-28 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.9686 | Diamond | I24 |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | Silicon nitride chips | fixed target |
| Measurement |
|---|
| Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
|---|
| 1 | undefined (fs) | | | undefined (KeV) | |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.73 | 44.7 | 100 | 0.916 | 0.959 | 0.183 | 2.48 | 51.4 | | 74214 | | | |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 1.73 | 1.76 | 100 | | 0.893 | 0.492 | 0.714 | 0.58 | | |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1.73 | 37.398 | 1.35 | 74204 | 2005 | 99.99 | 0.1789 | 0.1774 | 0.2337 | |
| 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 | 7.887 |
| f_angle_d | 0.831 |
| f_chiral_restr | 0.048 |
| f_bond_d | 0.007 |
| f_plane_restr | 0.005 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 5542 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 525 |
| Heterogen Atoms | 86 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| DENZO | data reduction |
| cctbx.prime | data scaling |
| MOLREP | phasing |
