6D0P
1.88 Angstrom Resolution Crystal Structure of Quercetin 2,3-dioxygenase from Acinetobacter baumannii
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 292 | 8.5 mg/mL protein in 0.01 M Tris, pH 8.3, screen: Classics II (H1) (0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 8.5, 25% w/v PEG3350) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.86 | 57 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 95.481 | α = 90 |
b = 131.977 | β = 103.58 |
c = 123.987 | 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 | CCD | RAYONIX MX-300 | C(111) | 2018-03-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (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 | 1.88 | 30 | 99.9 | 0.094 | 0.094 | 0.107 | 0.05 | 15.7 | 4.5 | 120737 | -3 | 24.4 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 1.88 | 1.91 | 100 | 0.763 | 0.763 | 0.865 | 0.404 | 0.649 | 2.1 | 4.4 |
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 | SAD | THROUGHOUT | 1.88 | 29.81 | 114778 | 5945 | 99.8 | 0.15975 | 0.15821 | 0.19039 | RANDOM | 27.715 |
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] | |
0.03 | -0.41 | 0.33 | -0.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.251 |
r_sphericity_bonded | 31.152 |
r_sphericity_free | 21.502 |
r_dihedral_angle_4_deg | 10.707 |
r_dihedral_angle_3_deg | 9.89 |
r_long_range_B_refined | 6.436 |
r_long_range_B_other | 6.285 |
r_dihedral_angle_1_deg | 4.323 |
r_scangle_other | 3.772 |
r_scbond_it | 2.428 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8912 |
Nucleic Acid Atoms | |
Solvent Atoms | 1056 |
Heterogen Atoms | 101 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
HKL-3000 | phasing |