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Crystal structure of Group 1 Oligosaccharide-releasing beta-N-acetylgalactosaminidase NgaCa from Cohnella abietis, apo 2 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 Magnesium chloride hexahydrate, 0.1 M Bis-Tris pH 6.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.18 43.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.214 α = 88.41 b = 69.679 β = 74.33 c = 71.113 γ = 87.93
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 2022-06-17 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) R Merge I (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 48.36 97.1 0.093 0.963 7.1 3.5 96240
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 0.872
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 47.67 91414 4810 97.08 0.15755 0.1557 0.1691 0.19253 0.2029 RANDOM 16.853
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] 1.52 0.25 -0.29 -0.35 0.1 -1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.666 r_dihedral_angle_2_deg 12.791 r_dihedral_angle_1_deg 6.766 r_long_range_B_refined 5.731 r_long_range_B_other 5.638 r_scangle_other 4.451 r_scbond_it 2.856 r_scbond_other 2.856 r_mcangle_other 2.756 r_mcangle_it 2.755
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.666 r_dihedral_angle_2_deg 12.791 r_dihedral_angle_1_deg 6.766 r_long_range_B_refined 5.731 r_long_range_B_other 5.638 r_scangle_other 4.451 r_scbond_it 2.856 r_scbond_other 2.856 r_mcangle_other 2.756 r_mcangle_it 2.755 r_mcbond_it 1.835 r_mcbond_other 1.834 r_angle_refined_deg 1.66 r_angle_other_deg 0.566 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 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 8060 Nucleic Acid Atoms Solvent Atoms 694 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing