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Structure of STG-hydrolyzing beta-glucosidase 1 (PSTG1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 PEG 3000, imidazole, lithium sulfate
Crystal Properties Matthews coefficient Solvent content 3.3 62.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.3 α = 71.468 b = 113.25 β = 82.684 c = 158.66 γ = 79.83
Diffraction Diffraction Experiment 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 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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) 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 0.232 0.2817 0.2823 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 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
RMS Deviations 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 r_scbond_it 1.702 r_scbond_other 1.702 r_angle_refined_deg 1.648 r_mcbond_it 1.592 r_mcbond_other 1.592 r_angle_other_deg 0.856 r_nbd_other 0.244 r_symmetry_nbd_refined 0.243 r_symmetry_nbd_other 0.233 r_nbd_refined 0.212 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.186 r_ncsr_local_group_2 0.125 r_ncsr_local_group_5 0.125 r_ncsr_local_group_4 0.123 r_ncsr_local_group_3 0.122 r_ncsr_local_group_1 0.12 r_ncsr_local_group_6 0.12 r_symmetry_xyhbond_nbd_refined 0.115 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.072 r_symmetry_xyhbond_nbd_other 0.067 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23104 Nucleic Acid Atoms Solvent Atoms 491 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction XDS data scaling MOLREP phasing