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Crystal structure of Group 2Oligosaccharide/Monosaccharide-releasing beta-N-acetylhexosaminidase NgaAt from Arabidopsis thaliana 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 Magnesium chloride hexahydrate, 0.1 M Hepes-Na pH 7.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.38 48.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.852 α = 90 b = 134.036 β = 90 c = 149.969 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 9M 2021-10-22 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 2.2 48.07 100 0.997 9.5 13.6 71289
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 2.2 2.25 0.648
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 2.2 48.07 67508 3690 99.95 0.17206 0.16892 0.22947 0.2302 RANDOM 43.8
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] 2.97 -2.87 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.927 r_dihedral_angle_2_deg 16.81 r_long_range_B_other 10.286 r_long_range_B_refined 10.275 r_scangle_other 8.613 r_dihedral_angle_1_deg 7.964 r_mcangle_other 7.18 r_mcangle_it 7.179 r_scbond_it 6.551 r_scbond_other 6.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.927 r_dihedral_angle_2_deg 16.81 r_long_range_B_other 10.286 r_long_range_B_refined 10.275 r_scangle_other 8.613 r_dihedral_angle_1_deg 7.964 r_mcangle_other 7.18 r_mcangle_it 7.179 r_scbond_it 6.551 r_scbond_other 6.55 r_mcbond_it 5.558 r_mcbond_other 5.558 r_angle_refined_deg 2.11 r_angle_other_deg 0.686 r_chiral_restr 0.095 r_bond_refined_d 0.014 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 8941 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing