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Crystal structure of UDP/mannose-bound AGO61/beta-1,4-N-Acetylglucosaminyltransferase 2 (POMGNT2)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 12% PEG4000, 0.1 M sodium citrate tribasic (pH 6.0), and 0.1 M sodium chloride
Crystal Properties Matthews coefficient Solvent content 4.05 69.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.019 α = 90 b = 150.002 β = 90 c = 191.481 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 16M 2020-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
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 2.8 50 99.7 0.062 0.999 13.5 3.6 97911
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.97 99.3 0.918 0.569 1.2 3.4
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 SAD THROUGHOUT 2.8 47.92 97911 5042 99.85 0.19304 0.19124 0.22823 0.2117 RANDOM 88.647
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] -4.61 6.09 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.411 r_dihedral_angle_4_deg 21.248 r_dihedral_angle_3_deg 19.316 r_long_range_B_refined 15.806 r_long_range_B_other 15.806 r_scangle_other 13.484 r_mcangle_it 11.13 r_mcangle_other 11.13 r_scbond_it 9.221 r_scbond_other 9.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.411 r_dihedral_angle_4_deg 21.248 r_dihedral_angle_3_deg 19.316 r_long_range_B_refined 15.806 r_long_range_B_other 15.806 r_scangle_other 13.484 r_mcangle_it 11.13 r_mcangle_other 11.13 r_scbond_it 9.221 r_scbond_other 9.22 r_mcbond_it 8.046 r_mcbond_other 8.045 r_dihedral_angle_1_deg 8.007 r_angle_refined_deg 1.634 r_angle_other_deg 1.226 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 16633 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 236
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling AutoSol phasing