7RGE
Crystal structure of phosphoadenylyl-sulfate (PAPS) reductase from Candida auris, phosphate complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2OQ2 | PDB entry 2OQ2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 298 | 0.1 M sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v PEG3350, 1 mM AMP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.89 | 57.43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 109.508 | α = 90 |
b = 132 | β = 90 |
c = 44.617 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | 100 | IMAGE PLATE | RIGAKU RAXIS IV | 2019-11-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.38 | 30 | 100 | 0.059 | 0.027 | 24.78 | 6 | 13451 | 57.32 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.38 | 2.42 | 0.863 | 0.437 | 0.875 | 1.06 |
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 | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | PDB entry 2OQ2 | 2.38 | 28.26 | 1.36 | 13441 | 673 | 99.92 | 0.1877 | 0.1859 | 0.2211 | RANDOM | 70.8 |
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 |
f_dihedral_angle_d | 22.4866 |
f_angle_d | 0.5823 |
f_chiral_restr | 0.0428 |
f_plane_restr | 0.0048 |
f_bond_d | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1632 |
Nucleic Acid Atoms | |
Solvent Atoms | 105 |
Heterogen Atoms | 17 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHASER | phasing |
PHENIX | model building |
Coot | model building |