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SGL a GH20 family sulfoglycosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold alphafold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 23.7 mg/mL protein in the buffer of Tris-HCl 25 mM, pH 8.0, and NaCl 200 mM was mixed 1:1 with the precipitant containing 0.1 M Bis-tris, pH 6.5, and 18-21.5% w/v PEG5000 MME.
Crystal Properties Matthews coefficient Solvent content 5.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.95 α = 90 b = 133.42 β = 90 c = 225.37 γ = 90
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 2019-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.71 94.18 97.6 0.981 5.1 1.9 406028
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.71 2.77 97.8 0.343 1.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE alphafold 2.711 94.176 406022 20528 96.588 0.285 0.283 0.3187 25.682
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] 0.498 1.226 -6.7 -16.627 -0.939 16.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.604 r_dihedral_angle_6_deg 14.494 r_dihedral_angle_1_deg 13.098 r_dihedral_angle_2_deg 10.523 r_lrange_it 4.545 r_lrange_other 4.545 r_mcangle_it 2.928 r_mcangle_other 2.928 r_scangle_it 2.156 r_scangle_other 2.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.604 r_dihedral_angle_6_deg 14.494 r_dihedral_angle_1_deg 13.098 r_dihedral_angle_2_deg 10.523 r_lrange_it 4.545 r_lrange_other 4.545 r_mcangle_it 2.928 r_mcangle_other 2.928 r_scangle_it 2.156 r_scangle_other 2.156 r_mcbond_it 1.863 r_mcbond_other 1.863 r_angle_refined_deg 1.761 r_scbond_it 1.401 r_scbond_other 1.401 r_angle_other_deg 0.587 r_nbd_other 0.37 r_symmetry_xyhbond_nbd_refined 0.351 r_symmetry_nbd_refined 0.339 r_nbd_refined 0.338 r_xyhbond_nbd_refined 0.309 r_symmetry_nbd_other 0.254 r_ncsr_local_group_4 0.248 r_ncsr_local_group_5 0.248 r_ncsr_local_group_6 0.248 r_ncsr_local_group_3 0.247 r_ncsr_local_group_1 0.246 r_ncsr_local_group_2 0.244 r_ncsr_local_group_7 0.244 r_nbtor_refined 0.204 r_ncsr_local_group_24 0.173 r_ncsr_local_group_12 0.171 r_ncsr_local_group_9 0.167 r_ncsr_local_group_21 0.167 r_ncsr_local_group_19 0.166 r_ncsr_local_group_23 0.166 r_ncsr_local_group_10 0.165 r_ncsr_local_group_26 0.165 r_ncsr_local_group_8 0.164 r_ncsr_local_group_11 0.163 r_ncsr_local_group_14 0.163 r_ncsr_local_group_15 0.163 r_ncsr_local_group_20 0.163 r_ncsr_local_group_17 0.161 r_ncsr_local_group_25 0.16 r_ncsr_local_group_16 0.158 r_ncsr_local_group_28 0.158 r_ncsr_local_group_13 0.156 r_ncsr_local_group_22 0.154 r_ncsr_local_group_27 0.153 r_symmetry_xyhbond_nbd_other 0.152 r_ncsr_local_group_18 0.15 r_symmetry_nbtor_other 0.092 r_chiral_restr 0.081 r_gen_planes_refined 0.012 r_bond_refined_d 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 31754 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing