Dye type peroxidase Aa from Streptomyces lividans: 196 kGy structure
Serial Crystallography (SX)
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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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 |
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Matthews coefficient | Solvent content |
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2.28 | 46.16 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 73.057 | α = 90 |
b = 68.37 | β = 105.81 |
c = 75.033 | γ = 90 |
Symmetry |
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Space Group | P 1 21 1 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | x-ray | 293 | PIXEL | DECTRIS PILATUS3 6M | | 2018-06-28 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.9686 | Diamond | I24 |
Serial Crystallography
Sample delivery method |
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Diffraction ID | Description | Sample Delivery Method |
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1 | Silicon nitride chips | fixed target |
Measurement |
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Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
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1 | undefined (fs) | | | undefined (KeV) | |
Data Collection
Overall |
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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 |
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1 | 1.82 | 44.7 | 100 | 0.851 | 0.966 | 0.174 | 2.43 | 46 | | 64459 | | | |
Highest Resolution Shell |
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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) |
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1 | 1.82 | 1.85 | 99.5 | | 0.864 | 0.506 | 0.75 | 0.55 | 10.9 | |
Refinement
Statistics |
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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 |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.82 | 37.383 | 1.34 | 63829 | 2010 | 99.96 | 0.1816 | 0.1798 | 0.2359 | 29.0933 |
Temperature Factor Modeling |
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
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| | | | | |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 5542 |
Nucleic Acid Atoms | |
Solvent Atoms | 438 |
Heterogen Atoms | 146 |
Software
Software |
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Software Name | Purpose |
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PHENIX | refinement |
PDB_EXTRACT | data extraction |
DIALS | data reduction |
cctbx.prime | data scaling |
MOLREP | phasing |