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Crystal structure of Group 3 Oligosaccharide/Monosaccharide-releasing beta-N-acetylgalactosaminidase NgaDssm, apo form
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 2.44 49.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.379 α = 90 b = 53.379 β = 90 c = 427.352 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 2022-07-02 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 47.8 100 0.997 10.6 23 64770
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 0.688
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 1.76 47.8 59829 3242 98.91 0.18162 0.17996 0.1939 0.21268 0.2253 RANDOM 22.91
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] 0.37 0.37 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.118 r_dihedral_angle_2_deg 11.119 r_long_range_B_refined 7.294 r_long_range_B_other 7.218 r_dihedral_angle_1_deg 6.854 r_scangle_other 6.1 r_scbond_it 4.362 r_scbond_other 4.294 r_mcangle_it 3.396 r_mcangle_other 3.396
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.118 r_dihedral_angle_2_deg 11.119 r_long_range_B_refined 7.294 r_long_range_B_other 7.218 r_dihedral_angle_1_deg 6.854 r_scangle_other 6.1 r_scbond_it 4.362 r_scbond_other 4.294 r_mcangle_it 3.396 r_mcangle_other 3.396 r_mcbond_it 2.567 r_mcbond_other 2.565 r_angle_refined_deg 1.966 r_angle_other_deg 0.696 r_chiral_restr 0.108 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 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 4302 Nucleic Acid Atoms Solvent Atoms 401 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing