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Crystal structure of Flavihumibacter petaseus GH31 alpha-galactosidase in complex with galactose
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 3.08 60.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.357 α = 101.822 b = 72.371 β = 105.114 c = 80.884 γ = 103.668
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 2022-06-25 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) 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 2.15 46.01 98 0.097 0.138 0.993 9.9 3.5 77597
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 2.15 2.19 97.1 0.487 0.689 0.487 0.739 2.1 3.5
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 2.15 43.695 77593 3948 97.972 0.155 0.152 0.1567 0.2224 0.2239 34.168
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] 0.842 0.745 0.738 -0.828 0.221 -0.705
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.395 r_dihedral_angle_3_deg 15.267 r_dihedral_angle_2_deg 9.488 r_dihedral_angle_1_deg 7.099 r_lrange_it 4.15 r_lrange_other 4.11 r_rigid_bond_restr 3.81 r_scangle_it 3.29 r_scangle_other 3.29 r_mcangle_it 2.957
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.395 r_dihedral_angle_3_deg 15.267 r_dihedral_angle_2_deg 9.488 r_dihedral_angle_1_deg 7.099 r_lrange_it 4.15 r_lrange_other 4.11 r_rigid_bond_restr 3.81 r_scangle_it 3.29 r_scangle_other 3.29 r_mcangle_it 2.957 r_mcangle_other 2.957 r_scbond_it 2.292 r_scbond_other 2.291 r_mcbond_it 2.057 r_mcbond_other 2.056 r_angle_refined_deg 1.439 r_angle_other_deg 0.496 r_symmetry_nbd_refined 0.253 r_nbd_other 0.23 r_nbd_refined 0.208 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.137 r_symmetry_xyhbond_nbd_refined 0.108 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.067 r_symmetry_xyhbond_nbd_other 0.051 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8114 Nucleic Acid Atoms Solvent Atoms 386 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing