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alpha-1,2-glucosidase from Arthrobacter humicola A8F5, glucose 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 2.21 44.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.458 α = 90 b = 107.09 β = 90 c = 110.403 γ = 90
Symmetry Space Group P 21 21 21
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 2M-F 2023-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1 Photon Factory AR-NE3A
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 1.9 49.07 100 0.102 0.111 0.998 7.9 6.6 98048 25.8
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 1.9 1.93 100 1.136 1.237 0.621 1.7 6.4
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 1.9 49.07 93333 4623 99.98 0.21757 0.2154 0.2247 0.26311 0.2681 RANDOM 34.9
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] -2.05 2.09 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.661 r_dihedral_angle_2_deg 11.908 r_long_range_B_refined 8.106 r_long_range_B_other 8.105 r_dihedral_angle_1_deg 7.262 r_scangle_other 6.235 r_mcangle_it 5.178 r_mcangle_other 5.178 r_scbond_it 4.256 r_scbond_other 4.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.661 r_dihedral_angle_2_deg 11.908 r_long_range_B_refined 8.106 r_long_range_B_other 8.105 r_dihedral_angle_1_deg 7.262 r_scangle_other 6.235 r_mcangle_it 5.178 r_mcangle_other 5.178 r_scbond_it 4.256 r_scbond_other 4.256 r_mcbond_it 3.607 r_mcbond_other 3.607 r_angle_refined_deg 1.94 r_angle_other_deg 0.641 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 9130 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing