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Crystal structure of Group 3 Oligosaccharide/Monosaccharide-releasing beta-N-acetylgalactosaminidase NgaDssm in complex with GalNAc-thiazoline
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 293.15 0.2 M Lithium sulfate, 0.1 M Bis-Tris pH 6.0, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.46 50.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.537 α = 90 b = 53.537 β = 90 c = 428.292 γ = 90
Symmetry Space Group P 43 21 2
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 9M 2022-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0000 SPring-8 BL32XU
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 1.75 47.93 100 0.994 8.7 23.2 65283
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 1.75 1.78 0.629
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 1.75 47.93 61753 3313 99.95 0.17739 0.17587 0.1875 0.20584 0.2173 RANDOM 22.793
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] -0.14 -0.14 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.759 r_dihedral_angle_2_deg 8.367 r_dihedral_angle_1_deg 6.527 r_long_range_B_refined 6.191 r_long_range_B_other 6.093 r_scangle_other 5.016 r_scbond_it 3.34 r_scbond_other 3.328 r_mcangle_it 2.765 r_mcangle_other 2.765
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.759 r_dihedral_angle_2_deg 8.367 r_dihedral_angle_1_deg 6.527 r_long_range_B_refined 6.191 r_long_range_B_other 6.093 r_scangle_other 5.016 r_scbond_it 3.34 r_scbond_other 3.328 r_mcangle_it 2.765 r_mcangle_other 2.765 r_mcbond_it 2.013 r_mcbond_other 2.013 r_angle_refined_deg 1.638 r_angle_other_deg 0.556 r_chiral_restr 0.083 r_bond_refined_d 0.01 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4322 Nucleic Acid Atoms Solvent Atoms 401 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing