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Crystal structure of GH31 family Sulfoquinovosidase BmSQase in covalent complex with SQ-aziridine (SQZ)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OHS
Crystallization Crystalization Experiments 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 Matthews coefficient Solvent content 2.22 44.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.524 α = 90 b = 194.726 β = 92.29 c = 117.654 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 XE 16M 2021-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97624 Diamond I03
Data Collection Overall 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 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 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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) 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 0.2165 0.24405 0.2465 RANDOM 29.234
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] -0.28 -1.62 0.99 -0.58
RMS Deviations 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
RMS Deviations 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 r_mcbond_it 2.882 r_mcbond_other 2.881 r_angle_refined_deg 1.525 r_angle_other_deg 0.568 r_chiral_restr 0.178 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21281 Nucleic Acid Atoms Solvent Atoms 587 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction MOLREP phasing