8T5W
Influenza PAN endonuclease I38T mutant with Baloxavir
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 8DDB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 306 | 32% PEG (MW 4000 g/mol), 100 mM Tris (pH 8.35), and 220 mM sodium acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.77 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 75.111 | α = 90 |
b = 75.111 | β = 90 |
c = 121.444 | γ = 120 |
Symmetry | |
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Space Group | P 62 2 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 PILATUS3 6M | 2021-10-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.1 | 1.000 | ALS | 8.2.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.65 | 57.34 | 99.9 | 0.054 | 0.999 | 28 | 20.7 | 46072 | 32.56 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.65 | 1.71 | 0.861 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.65 | 57.34 | 1.33 | 46071 | 3678 | 99.84 | 0.2044 | 0.2019 | 0.2339 | 40.4 |
Temperature Factor Modeling | ||||||
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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 | 9.3885 |
f_angle_d | 1.5533 |
f_chiral_restr | 0.1061 |
f_plane_restr | 0.0089 |
f_bond_d | 0.0086 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1463 |
Nucleic Acid Atoms | |
Solvent Atoms | 95 |
Heterogen Atoms | 70 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
xia2 | data reduction |
Aimless | data scaling |
PHASER | phasing |