Dye type peroxidase Aa from Streptomyces lividans: imidazole complex
Serial Crystallography (SX)
Starting Model(s)
Initial Refinement Model(s) |
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Type | Source | Accession Code | Details |
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experimental model | PDB | 5MAP | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | BATCH MODE | 7 | 291 | 1:1 ratio of a 6.5 mg/ml DtpAa protein solution with precipitant solution containing 20% PEG 6000, 100 mM HEPES pH 7.0 |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.22 | 44.59 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 72.48 | α = 90 |
b = 68.03 | β = 105.57 |
c = 73.53 | 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 | 301 | CCD | MPCCD | | 2017-10-10 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | FREE ELECTRON LASER | SACLA BEAMLINE BL2 | 1.24 | SACLA | BL2 |
Serial Crystallography
Sample delivery method |
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Diffraction ID | Description | Sample Delivery Method |
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1 | Silicon nitride chip | fixed target |
Fixed Target |
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Diffraction ID | Description | Sample Holding | Support Base | Motion control | Details | Sample Solvent |
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1 | | | | | | Mother liquor |
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 | 10 (fs) | 30 | 1.66 | 10.01 (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 | 1.88 | 37 | 100 | 0.224 | 0.96 | 0.158 | 5.7 | 102 | | 56220 | | | |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 1.88 | 1.93 | 100 | | 0.6 | 0.639 | 1.54 | | |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | 5map | 1.88 | 35.295 | 1.34 | 56150 | 2830 | 99.96 | 0.1404 | 0.1385 | 0.1766 | 30.8175 |
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 | 5467 |
Nucleic Acid Atoms | |
Solvent Atoms | 414 |
Heterogen Atoms | 165 |
Software
Software |
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Software Name | Purpose |
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PHENIX | refinement |
PDB_EXTRACT | data extraction |
CrystFEL | data reduction |
CrystFEL | data scaling |
MOLREP | phasing |