8J9F
Structure of STG-hydrolyzing beta-glucosidase 1 (PSTG1)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293 | PEG 3000, imidazole, lithium sulfate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.3 | 62.72 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 65.3 | α = 71.468 |
b = 113.25 | β = 82.684 |
c = 158.66 | γ = 79.83 |
Symmetry | |
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Space Group | P 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 | 80 | PIXEL | DECTRIS EIGER X 9M | 2021-06-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL32XU | 1.0 | SPring-8 | BL32XU |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.85 | 50 | 99.6 | 0.619 | 0.879 | 3.65 | 8.46 | 832650 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.85 | 3.02 | 99.8 | 1.661 | 0.515 | 1.33 | 8.25 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.85 | 47.6 | 98461 | 5067 | 99.681 | 0.234 | 0.2317 | 0.2817 | Random selection | 19.839 |
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] | |
-1.229 | -0.629 | -0.115 | 1.792 | 1.404 | -0.033 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 17.764 |
r_dihedral_angle_3_deg | 17.346 |
r_dihedral_angle_1_deg | 6.043 |
r_lrange_it | 5.639 |
r_lrange_other | 5.638 |
r_dihedral_angle_2_deg | 3.645 |
r_scangle_it | 2.955 |
r_scangle_other | 2.955 |
r_mcangle_it | 2.696 |
r_mcangle_other | 2.696 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 23104 |
Nucleic Acid Atoms | |
Solvent Atoms | 491 |
Heterogen Atoms | 18 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
MOLREP | phasing |