☰ Navigation Tabs
alpha-1,2-glucosidase from Arthrobacter humicola A8F5, kojitriose complex
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 2.37 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.385 α = 90 b = 107.985 β = 93.34 c = 105.522 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 PILATUS 6M 2025-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1 SPring-8 BL45XU
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 1.83 48.49 99.8 0.267 0.277 0.995 7.8 14.1 111405 28.3
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 1.83 1.86 96.9 3.16 3.277 0.567 1 14.3
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 1.83 48.49 105886 5479 99.84 0.21272 0.21046 0.2204 0.2572 0.2668 RANDOM 35.594
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] 2.72 -0.58 -0.14 -2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.596 r_dihedral_angle_2_deg 11.326 r_long_range_B_refined 9.403 r_long_range_B_other 9.403 r_dihedral_angle_1_deg 7.788 r_scangle_other 7.539 r_mcangle_it 6.238 r_mcangle_other 6.238 r_scbond_it 5.485 r_scbond_other 5.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.596 r_dihedral_angle_2_deg 11.326 r_long_range_B_refined 9.403 r_long_range_B_other 9.403 r_dihedral_angle_1_deg 7.788 r_scangle_other 7.539 r_mcangle_it 6.238 r_mcangle_other 6.238 r_scbond_it 5.485 r_scbond_other 5.484 r_mcbond_it 4.655 r_mcbond_other 4.644 r_angle_refined_deg 2.337 r_angle_other_deg 0.812 r_chiral_restr 0.125 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 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 9162 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing