3PT2
Structure of a viral OTU domain protease bound to Ubiquitin
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 294 | 27% PEG4000, 0.1 M sodium acetate, 0.21 M ammonium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
2 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 294 | 27% PEG6000, 0.1 M sodium acetate, 0.21 M ammonium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 146.01 | α = 90 |
b = 146.01 | β = 90 |
c = 58.14 | γ = 120 |
Symmetry | |
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Space Group | P 62 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | RAYONIX MX300HE | Vertical collimating mirror, DCM with indirectly water-cooled first crystal, Toroidal focusing mirror | 2008-05-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | 0.9796 | CLSI | 08ID-1 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.5 | 52.8 | 99.9 | 0.093 | 13.1 | 7.1 | 13133 | 13116 | 3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.5 | 2.64 | 100 | 0.401 | 0.465 | 5.2 | 7.3 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | 2.5 | 47.793 | 13116 | 12872 | 1289 | 98.13 | 0.1699 | 0.1637 | 0.2242 | RANDOM |
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] | |
-0.3689 | -0.3689 | 0.7378 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.107 |
f_angle_d | 0.906 |
f_chiral_restr | 0.057 |
f_bond_d | 0.006 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1913 |
Nucleic Acid Atoms | |
Solvent Atoms | 105 |
Heterogen Atoms | 23 |
Software
Software | |
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Software Name | Purpose |
MxDC | data collection |
SOLVE | phasing |
PHENIX | refinement |
MOSFLM | data reduction |
SCALA | data scaling |