Dye type peroxidase Aa from Streptomyces lividans: 235.2 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 = 73.066 | α = 90 |
| b = 68.377 | β = 105.84 |
| c = 75.079 | 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 | 1.93 | 44.7 | 100 | 0.806 | 0.966 | 0.172 | 2.28 | 46.5 | | 54263 | | | |
| 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 | 1.93 | 1.96 | 99.8 | | 0.874 | 0.544 | 0.791 | 0.47 | 12.7 | |
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 | THROUGHOUT | 1.93 | 37.385 | 1.35 | 53662 | 2010 | 99.97 | 0.1824 | 0.1803 | 0.18 | 0.2356 | 0.24 | 31.8232 |
| 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] |
|---|
| | | | | |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 5542 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 291 |
| Heterogen Atoms | 146 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| DIALS | data reduction |
| cctbx.prime | data scaling |
| MOLREP | phasing |