7PBG
4-ethylphenol oxidase from Gulosibacter chungangensis: native structure
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5FXD |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 293 | 0.1 M Trizma pH 8.0, 24% PEG 6000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.43 | 48 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 151.134 | α = 90 |
b = 96.08 | β = 115.65 |
c = 87.636 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | 100 | PIXEL | DECTRIS EIGER X 16M | 2021-04-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 0.999869 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.6 | 44.23 | 94.5 | 0.083 | 0.092 | 0.039 | 0.996 | 9.8 | 4.9 | 140211 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.6 | 1.63 | 86.4 | 0.642 | 0.738 | 0.353 | 0.71 | 3.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | 5FXD | 1.6 | 44.23 | 133003 | 6975 | 94.27 | 0.1822 | 0.1809 | 0.2066 | RANDOM | 21.958 |
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] | |
0.63 | 0.54 | -1.62 | 0.33 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.36 |
r_dihedral_angle_4_deg | 22.026 |
r_dihedral_angle_3_deg | 11.928 |
r_dihedral_angle_1_deg | 6.681 |
r_angle_refined_deg | 1.655 |
r_angle_other_deg | 1.535 |
r_chiral_restr | 0.087 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.011 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8200 |
Nucleic Acid Atoms | |
Solvent Atoms | 924 |
Heterogen Atoms | 108 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |