5XQ2
Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 5A6 on the guide strand
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 308 | 2.8 M Na-acetate, pH7.0, 0.1M Tris-Cl, pH 8.0 and 0.15 M glycine |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.8 | 67.61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 201.843 | α = 90 |
b = 201.843 | β = 90 |
c = 201.843 | γ = 90 |
Symmetry | |
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Space Group | P 21 3 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 S 6M | 2017-01-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL19U1 | 0.97852 | SSRF | BL19U1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 3.32 | 50 | 100 | 0.106 | 45.5 | 33.8 | 40665 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 3.32 | 3.38 | 100 | 0.908 | 4.2 | 26.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 4KPY | 3.33 | 48.95 | 2.15 | 37315 | 1846 | 92.1 | 0.254 | 0.252 | 0.294 |
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 | 24.689 |
f_angle_d | 1.703 |
f_chiral_restr | 0.144 |
f_bond_d | 0.013 |
f_plane_restr | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10369 |
Nucleic Acid Atoms | 1470 |
Solvent Atoms | 3 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-2000 | data processing |
HKL-2000 | data scaling |
PHASER | phasing |