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Crystal structure of Flavihumibacter petaseus GH31 alpha-galactosidase mutant D304A in complex with alpha-1,4-galactobiose
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 6 293 1 M sodium chloride, 50 mM MES-NaOH, pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.12 60.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.499 α = 101.922 b = 72.543 β = 104.396 c = 81.202 γ = 103.708
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 2023-03-10 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 1.9 46.044 97.4 0.071 0.101 0.071 0.997 7.8 3.5 113161
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 1.9 1.93 0.591 0.699 0.494 0.769 1.6
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 1.9 46.044 113160 5585 97.443 0.139 0.1361 0.1354 0.1922 0.1934 23.858
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] 1.449 -0.253 -1.694 0.213 0.206 -0.423
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.142 r_dihedral_angle_3_deg 14.546 r_dihedral_angle_2_deg 9.247 r_dihedral_angle_1_deg 6.786 r_rigid_bond_restr 5.543 r_lrange_it 3.669 r_lrange_other 3.581 r_scangle_it 3.248 r_scangle_other 3.248 r_mcangle_other 2.642
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.142 r_dihedral_angle_3_deg 14.546 r_dihedral_angle_2_deg 9.247 r_dihedral_angle_1_deg 6.786 r_rigid_bond_restr 5.543 r_lrange_it 3.669 r_lrange_other 3.581 r_scangle_it 3.248 r_scangle_other 3.248 r_mcangle_other 2.642 r_mcangle_it 2.639 r_scbond_it 2.378 r_scbond_other 2.378 r_mcbond_it 1.949 r_mcbond_other 1.948 r_angle_refined_deg 1.623 r_angle_other_deg 0.566 r_symmetry_nbd_refined 0.341 r_nbd_refined 0.221 r_nbd_other 0.22 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.186 r_symmetry_xyhbond_nbd_refined 0.176 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_other 0.047 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8091 Nucleic Acid Atoms Solvent Atoms 794 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing