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Structure of AauA, a sugar-binding protein with its substrate
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 293 10% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.07 40.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.38 α = 90 b = 66.94 β = 94.45 c = 57.85 γ = 90
Symmetry Space Group C 1 2 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 EIGER2 XE 16M 2024-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.96860 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.35 38.9 79.1 0.028 1 29.8 6.2 50386
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.37 18.2 0.98 7.5 3.2
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.35 38.9 47791 2594 79.05 0.1272 0.12632 0.1435 0.1745 RANDOM 13.456
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] -0.36 0.24 0.58 -0.26
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 15.328 r_long_range_B_other 14.387 r_dihedral_angle_2_deg 12.476 r_dihedral_angle_3_deg 10.847 r_scangle_other 9.49 r_scbond_it 7.014 r_scbond_other 7.012 r_dihedral_angle_1_deg 6.25 r_mcangle_other 5.579 r_mcangle_it 5.578
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 15.328 r_long_range_B_other 14.387 r_dihedral_angle_2_deg 12.476 r_dihedral_angle_3_deg 10.847 r_scangle_other 9.49 r_scbond_it 7.014 r_scbond_other 7.012 r_dihedral_angle_1_deg 6.25 r_mcangle_other 5.579 r_mcangle_it 5.578 r_rigid_bond_restr 4.819 r_mcbond_it 3.888 r_mcbond_other 3.871 r_angle_refined_deg 2.022 r_angle_other_deg 0.69 r_chiral_restr 0.379 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2233 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing