8SLN
Crystal structure of Deinococcus geothermalis PprI complexed with ssDNA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3DTI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 298 | 0.3 M potassium sodium tartrate tetrahydrate, 20% polyethylene glycol 3350, and 2.5 mM MnCl2 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.28 | 46.17 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 84.99 | α = 90 |
b = 84.99 | β = 90 |
c = 88.55 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 | 95 | PIXEL | DECTRIS EIGER X 16M | 2020-05-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL17U1 | 0.9792 | SSRF | BL17U1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 2.2 | 30 | 99.7 | 0.035 | 0.038 | 0.9990000000000001 | 22.23 | 5.5 | 19166 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.2 | 2.26 | 0.484 | 0.535 | 0.9440000000000001 |
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 | 2.2 | 26.54 | 1.35 | 19049 | 927 | 99.21 | 0.2385 | 0.2371 | 0.2678 |
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 | 24.162 |
f_angle_d | 0.96 |
f_chiral_restr | 0.073 |
f_plane_restr | 0.009 |
f_bond_d | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1825 |
Nucleic Acid Atoms | 224 |
Solvent Atoms | |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XSCALE | data scaling |
HKL-2000 | data reduction |
PHASER | phasing |