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Crystal structure of Bacteroides salyersiae GH31 alpha-galactosidase
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 293 16% PEG 3350, 40 mM citric acid, 60 mM bis-tris propane
Crystal Properties Matthews coefficient Solvent content 3.03 59.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 200.521 α = 90 b = 157.535 β = 116.823 c = 131.408 γ = 90
Symmetry Space Group C 1 2 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 PILATUS3 S 6M 2022-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
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 3.5 48.635 99.9 0.168 0.199 0.106 0.996 9.3 6.8 45955
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 3.5 3.62 1.05 1.238 0.651 0.797 2
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.5 48.635 45953 2223 99.922 0.26 0.2569 0.265 0.3128 0.3237 102.778
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] 5.234 -4.531 7.794 -5.588
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 28.841 r_lrange_other 28.841 r_mcangle_it 19.997 r_mcangle_other 19.996 r_scangle_it 17.767 r_scangle_other 17.766 r_dihedral_angle_3_deg 16.858 r_dihedral_angle_2_deg 15.932 r_dihedral_angle_6_deg 15.217 r_mcbond_it 12.742
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 28.841 r_lrange_other 28.841 r_mcangle_it 19.997 r_mcangle_other 19.996 r_scangle_it 17.767 r_scangle_other 17.766 r_dihedral_angle_3_deg 16.858 r_dihedral_angle_2_deg 15.932 r_dihedral_angle_6_deg 15.217 r_mcbond_it 12.742 r_mcbond_other 12.741 r_scbond_it 11.05 r_scbond_other 11.05 r_dihedral_angle_1_deg 7.349 r_angle_refined_deg 1.498 r_angle_other_deg 0.481 r_ext_dist_refined_b 0.316 r_symmetry_nbd_refined 0.285 r_nbd_other 0.265 r_symmetry_nbd_other 0.214 r_nbd_refined 0.198 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.157 r_ncsr_local_group_2 0.114 r_ncsr_local_group_1 0.109 r_ncsr_local_group_4 0.107 r_ncsr_local_group_3 0.106 r_ncsr_local_group_9 0.101 r_ncsr_local_group_8 0.098 r_ncsr_local_group_5 0.097 r_ncsr_local_group_10 0.095 r_ncsr_local_group_7 0.089 r_ncsr_local_group_6 0.088 r_symmetry_xyhbond_nbd_other 0.087 r_symmetry_nbtor_other 0.085 r_symmetry_xyhbond_nbd_refined 0.077 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20611 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing