8PWY
Dye-decolourising peroxidase DtpB (112 kGy)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6YRD |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 293 | 6.2 mg/mL of protein in 20mM NaPi, 150mM NaCl pH 7 was mixed with 125 mM MgCl2, 125 mM HEPES, 18% PEG 4000 pH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.59 | 52.43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 86.771 | α = 90 |
b = 121.825 | β = 90 |
c = 199.518 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | 2019-09-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.9686 | Diamond | I24 |
Serial Crystallography
Fixed Target | ||||||
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Diffraction ID | Description | Sample Holding | Support Base | Motion control | Sample Solvent | |
1 | silicone chip |
Measurement | |||||
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Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
1 |
Data Reduction | |||
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Diffraction ID | Frames Indexed | Crystal Hits | Total Frames |
1 | 22905 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.8 | 40.07 | 100 | 0.979 | 0.134 | 2.06 | 68.1 | 195649 |
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) | ||||||||||
1 | 1.8 | 1.83 | 0.53 | 0.743 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.8 | 40.07 | 185679 | 9862 | 99.97 | 0.19954 | 0.19831 | 0.22287 | RANDOM | 29.434 |
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 | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 15.237 |
r_dihedral_angle_2_deg | 12.894 |
r_long_range_B_other | 8.381 |
r_long_range_B_refined | 8.374 |
r_scangle_other | 7.351 |
r_dihedral_angle_1_deg | 6.909 |
r_mcangle_it | 5.207 |
r_mcangle_other | 5.207 |
r_scbond_it | 4.951 |
r_scbond_other | 4.951 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14137 |
Nucleic Acid Atoms | |
Solvent Atoms | 395 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DIALS | data reduction |
DIALS | data scaling |
REFMAC | phasing |