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Engineered GH181 sialidase from Akkermansia muciniphila
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8AXT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 10% PEG 8000 W/V, 9% Ethylene glycol (v/v), 0.1M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.53 51.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.67 α = 90 b = 88.189 β = 90 c = 99.585 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 EIGER X 16M 2024-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.98 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.77 66.02 99 0.998 11.7 9.6 64414
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 1.77 1.8 0.503
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.77 66.02 64414 3267 99.473 0.157 0.1552 0.1953 0.2021 24.106
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] 0.045 0.647 -0.692
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.127 r_dihedral_angle_3_deg 13.187 r_dihedral_angle_1_deg 7.662 r_dihedral_angle_2_deg 6.963 r_lrange_it 6.56 r_lrange_other 6.417 r_scangle_it 5.063 r_scangle_other 5.062 r_scbond_it 3.386 r_scbond_other 3.385
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.127 r_dihedral_angle_3_deg 13.187 r_dihedral_angle_1_deg 7.662 r_dihedral_angle_2_deg 6.963 r_lrange_it 6.56 r_lrange_other 6.417 r_scangle_it 5.063 r_scangle_other 5.062 r_scbond_it 3.386 r_scbond_other 3.385 r_mcangle_it 2.992 r_mcangle_other 2.992 r_mcbond_it 2.166 r_mcbond_other 2.165 r_angle_refined_deg 1.519 r_angle_other_deg 0.515 r_symmetry_nbd_refined 0.228 r_nbd_refined 0.2 r_symmetry_nbd_other 0.194 r_nbd_other 0.182 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.167 r_symmetry_xyhbond_nbd_other 0.149 r_symmetry_xyhbond_nbd_refined 0.143 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4572 Nucleic Acid Atoms Solvent Atoms 566 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction TRUNCATE data scaling MOLREP phasing