8R56
Crystal structure of GH31 family Sulfoquinovosidase BmSQase in covalent complex with SQ-aziridine (SQZ)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 293 | A crystal of BmSQase was grown using a 30 mg mL-1 protein solution in buffer C, 0.15 uL protein. 0.15 uL mother liquor, the latter comprising 0.2 M KSCN and 20% w/v PEG (polyethylene glycol) 3350 in 0.1 M Bis-TRIS propane buffer pH 7.5. A stock solution of 1 was prepared at 10 mM in mother liquor. Crystals were soaked for 5 min with 0.3 ul of 1 to a final concentration of 3 mM. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.524 | α = 90 |
b = 194.726 | β = 92.29 |
c = 117.654 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 100 | PIXEL | DECTRIS EIGER2 XE 16M | 2021-09-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97624 | Diamond | I03 |
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 | 2.45 | 74.99 | 99.9 | 0.197 | 0.212 | 0.08 | 0.986 | 9.3 | 7.2 | 102876 |
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) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.45 | 2.49 | 100 | 1.174 | 1.267 | 0.474 | 0.637 | 7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2.45 | 62.55 | 97274 | 4989 | 99.37 | 0.21347 | 0.21188 | 0.24405 | RANDOM | 29.234 |
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] | |
-0.28 | -1.62 | 0.99 | -0.58 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 15.226 |
r_dihedral_angle_2_deg | 8.528 |
r_dihedral_angle_1_deg | 6.951 |
r_long_range_B_refined | 6.206 |
r_long_range_B_other | 6.195 |
r_scangle_other | 4.727 |
r_mcangle_it | 4.323 |
r_mcangle_other | 4.323 |
r_scbond_it | 3.063 |
r_scbond_other | 3.063 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 21281 |
Nucleic Acid Atoms | |
Solvent Atoms | 587 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
xia2 | data reduction |
MOLREP | phasing |