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Crystal structure of Group 4 Monosaccharide-releasing beta-N-acetylgalactosaminidase NgaP2 from Paenibacillus sp. TS12, 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 sodium Bromide, 0.1 M Bis-Tris pH 7.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.35 47.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.116 α = 90 b = 60.375 β = 120.08 c = 100.285 γ = 90
Symmetry Space Group C 1 2 1
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 2020-07-15 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 1.95 46.7 99.9 0.986 13.2 6.9 45106
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 1.95 2 0.541
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 1.95 46.7 42815 2287 99.9 0.14996 0.14764 0.161 0.19474 0.2084 RANDOM 20.259
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] -0.46 0.18 -0.31 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.064 r_dihedral_angle_2_deg 10.05 r_dihedral_angle_1_deg 7.05 r_long_range_B_refined 7.006 r_long_range_B_other 6.975 r_scangle_other 5.926 r_scbond_it 4.095 r_scbond_other 4.094 r_mcangle_it 3.049 r_mcangle_other 3.048
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.064 r_dihedral_angle_2_deg 10.05 r_dihedral_angle_1_deg 7.05 r_long_range_B_refined 7.006 r_long_range_B_other 6.975 r_scangle_other 5.926 r_scbond_it 4.095 r_scbond_other 4.094 r_mcangle_it 3.049 r_mcangle_other 3.048 r_mcbond_it 2.331 r_mcbond_other 2.33 r_angle_refined_deg 1.851 r_angle_other_deg 0.661 r_chiral_restr 0.107 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 4531 Nucleic Acid Atoms Solvent Atoms 368 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing