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Crystal structure of the thioredoxin domain of Amuc_2173 from Akkermansia muciniphila
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 7.5 289 0.2 M lithium sulfate, 0.1 M Tris-HCl, pH 7.5, and 24% (w/v) polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 1.76 30.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.662 α = 93.24 b = 44.534 β = 110.14 c = 45.714 γ = 114.86
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 2025-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL18U 0.9785 NFPSS BL18U
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 1.57 50 95.6 0.075 0.089 0.047 0.99 8.5 3.5 32585
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 1.57 1.63 88.7 0.359 0.432 0.236 0.877 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 (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 1.575 41.7 30502 1694 94.71 0.15655 0.15445 0.1654 0.19553 0.2079 RANDOM 14.732
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] 0.62 -0.4 0.23 0.01 0.1 -0.38
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 12.702 r_long_range_B_refined 12.581 r_dihedral_angle_3_deg 11.51 r_dihedral_angle_1_deg 6.772 r_scangle_other 6.643 r_mcangle_other 6.581 r_mcangle_it 6.58 r_scbond_it 4.382 r_scbond_other 4.381 r_dihedral_angle_2_deg 4.322
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 12.702 r_long_range_B_refined 12.581 r_dihedral_angle_3_deg 11.51 r_dihedral_angle_1_deg 6.772 r_scangle_other 6.643 r_mcangle_other 6.581 r_mcangle_it 6.58 r_scbond_it 4.382 r_scbond_other 4.381 r_dihedral_angle_2_deg 4.322 r_mcbond_it 4.107 r_mcbond_other 4.088 r_rigid_bond_restr 2.985 r_angle_refined_deg 1.553 r_angle_other_deg 0.541 r_chiral_restr 0.083 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 2144 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction PHASER phasing PDB_EXTRACT data extraction