6W2I
Crystal Structure of Y188G Variant of the Internal UBA Domain of HHR23A
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 2.0M Ammonium sulfate | |
2 | VAPOR DIFFUSION, SITTING DROP | 293 | 2.0M Ammonium sulfate |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 31.164 | α = 90 |
b = 31.164 | β = 90 |
c = 40.53 | γ = 90 |
Symmetry | |
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Space Group | P 43 |
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 PILATUS 6M | 2020-01-29 | M | SINGLE WAVELENGTH | ||||||
2 | 2 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2020-01-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.9795 | SSRL | BL9-2 |
2 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 1.77 | SSRL | BL9-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 1.45 | 31.16 | 98.95 | 0.07658 | 0.07961 | 0.02153 | 1 | 22.37 | 13.4 | 6875 | 11.23 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.45 | 1.502 | 97.84 | 0.5901 | 0.615 | 0.1703 | 0.926 | 4.34 | 12.5 |
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 | SAD | FREE R-VALUE | 1.45 | 31.16 | 1.36 | 6875 | 697 | 98.96 | 0.1532 | 0.1498 | 0.183 | 15.14 |
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 | 6.328 |
f_angle_d | 1.0683 |
f_chiral_restr | 0.0904 |
f_bond_d | 0.0112 |
f_plane_restr | 0.0068 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 369 |
Nucleic Acid Atoms | |
Solvent Atoms | 48 |
Heterogen Atoms | 6 |
Software
Software | |
---|---|
Software Name | Purpose |
Blu-Ice | data collection |
XDS | data reduction |
Aimless | data scaling |
HKL2Map | phasing |
AutoSol | phasing |
PHENIX | model building |
Coot | model building |
PHENIX | refinement |