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Crystal structure of Flavihumibacter petaseus 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 7 293 1 M sodium chloride, 50 mM MES-NaOH
Crystal Properties Matthews coefficient Solvent content 3.11 60.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.662 α = 101.741 b = 72.364 β = 104.955 c = 81.074 γ = 103.664
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 1.9 46.09 96.4 0.079 0.112 0.079 0.995 6.4 3.5 111441
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 77.4 0.437 0.618 0.437 0.77 1.5 3.3
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 44.415 111440 5490 96.38 0.139 0.1365 0.139 0.1808 0.1824 27.542
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] -0.168 -0.307 0.92 -1.226 0.392 0.532
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.867 r_dihedral_angle_3_deg 15.159 r_dihedral_angle_2_deg 8.874 r_dihedral_angle_1_deg 7.049 r_rigid_bond_restr 5.015 r_lrange_it 4.088 r_lrange_other 4.027 r_scangle_it 3.642 r_scangle_other 3.642 r_mcangle_other 2.865
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.867 r_dihedral_angle_3_deg 15.159 r_dihedral_angle_2_deg 8.874 r_dihedral_angle_1_deg 7.049 r_rigid_bond_restr 5.015 r_lrange_it 4.088 r_lrange_other 4.027 r_scangle_it 3.642 r_scangle_other 3.642 r_mcangle_other 2.865 r_mcangle_it 2.864 r_scbond_it 2.66 r_scbond_other 2.659 r_mcbond_it 2.148 r_mcbond_other 2.146 r_angle_refined_deg 1.62 r_angle_other_deg 0.557 r_symmetry_nbd_refined 0.3 r_nbd_other 0.252 r_nbd_refined 0.212 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.186 r_symmetry_xyhbond_nbd_refined 0.132 r_xyhbond_nbd_refined 0.131 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.077 r_bond_refined_d 0.012 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 8114 Nucleic Acid Atoms Solvent Atoms 654 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing