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alpha-1,2-glucosidase from Arthrobacter humicola A8F5
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, SITTING DROP 4.8 293 0.1 M sodium acetate pH5.1 , 34%(v/v)1,2-propanediol
Crystal Properties Matthews coefficient Solvent content 2.38 48.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.882 α = 90 b = 109.943 β = 93.66 c = 105.234 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 4M 2025-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.007 Photon Factory BL-1A
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 1.88 48.7 100 0.175 0.207 0.977 5 3.5 103014 17.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.91 100 0.928 1.092 0.536 1.5 3.6
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT AlphaFold 1.88 47.43 97766 5177 99.94 0.20943 0.2069 0.2201 0.25715 0.2645 RANDOM 23.775
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] 1.88 0.06 -0.75 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.493 r_dihedral_angle_2_deg 11.464 r_dihedral_angle_1_deg 7.539 r_long_range_B_refined 7.306 r_long_range_B_other 7.306 r_scangle_other 5.789 r_mcangle_it 4.279 r_mcangle_other 4.279 r_scbond_it 4.051 r_scbond_other 4.048
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.493 r_dihedral_angle_2_deg 11.464 r_dihedral_angle_1_deg 7.539 r_long_range_B_refined 7.306 r_long_range_B_other 7.306 r_scangle_other 5.789 r_mcangle_it 4.279 r_mcangle_other 4.279 r_scbond_it 4.051 r_scbond_other 4.048 r_mcbond_it 3.063 r_mcbond_other 3.059 r_angle_refined_deg 2.454 r_angle_other_deg 0.824 r_chiral_restr 0.118 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9195 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing