8Q22
Crystal structure of Vanadium-dependent haloperoxidase R425S mutant in complex with 1,3,5-trimethoxybenzene (A. marina)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5LPC | Crystal structure of Vanadium-dependent Haloperoxidase from A. marina |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293 | 0.1 M TRIS, 1.25 M ammoniumdihydrogenphosphate, 0.5 mM potassium vanadate, 10 mM 1,3,5-trimethoxybenzene |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.08 | 69.84 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 305.8 | α = 90 |
b = 305.8 | β = 90 |
c = 305.8 | γ = 90 |
Symmetry | |
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Space Group | F 41 3 2 |
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 | 2019-11-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.0 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 3.3 | 30 | 94.3 | 0.108 | 9.6 | 4.5 | 17934 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 3.3 | 3.4 | 0.629 | 2 |
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 | 3.3 | 30 | 17015 | 895 | 94.22 | 0.218 | 0.2163 | 0.2485 | RANDOM | 83.809 |
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_2_deg | 30.651 |
r_dihedral_angle_3_deg | 15.083 |
r_dihedral_angle_4_deg | 12.925 |
r_dihedral_angle_1_deg | 5.056 |
r_angle_refined_deg | 1.191 |
r_angle_other_deg | 1.046 |
r_rigid_bond_restr | 0.119 |
r_chiral_restr | 0.034 |
r_bond_refined_d | 0.002 |
r_gen_planes_refined | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4931 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 19 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
XSCALE | data scaling |
REFMAC | phasing |