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Crystal structure of DmC1GalT1 in complex with UDP-Mn2+ and the APD-TGalNAc-RP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q9NS00-F1 AF-Q9NS00-F1-model_v1.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 potassium thiocyanate, Polyethylene glycol monomethyl ether 2,000
Crystal Properties Matthews coefficient Solvent content 1.97 37.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.241 α = 90 b = 80.445 β = 93.19 c = 71.949 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 6M 2019-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9919 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.4 20 99.8 0.143 0.091 0.981 7.1 3.4 22437
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 0.825 0.526 0.412
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 AF-Q9NS00-F1-model_v1.pdb 2.4 20 21579 841 99.75 0.1778 0.17547 0.1827 0.23466 0.2379 RANDOM 32.346
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] 0.15 -2.71 0.25 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.386 r_dihedral_angle_4_deg 20.748 r_dihedral_angle_3_deg 17.226 r_dihedral_angle_1_deg 7.636 r_long_range_B_refined 7.613 r_long_range_B_other 7.613 r_scangle_other 5.665 r_mcangle_it 4.341 r_mcangle_other 4.341 r_scbond_it 3.622
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.386 r_dihedral_angle_4_deg 20.748 r_dihedral_angle_3_deg 17.226 r_dihedral_angle_1_deg 7.636 r_long_range_B_refined 7.613 r_long_range_B_other 7.613 r_scangle_other 5.665 r_mcangle_it 4.341 r_mcangle_other 4.341 r_scbond_it 3.622 r_scbond_other 3.622 r_mcbond_it 2.826 r_mcbond_other 2.825 r_angle_refined_deg 1.769 r_angle_other_deg 1.42 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.003 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 4570 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 178
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing