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Crystal structure of human GalNAc-T12 bound to a diglycosylated peptide, Mn2+, and UDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FFU PDB entry 2FFU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M sodium chloride, 20% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.58 52.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.82 α = 113.08 b = 73.123 β = 100.5 c = 74.441 γ = 108.23
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2017-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 2.007 20.03 97 0.197 0.1 4.7 1 163130 29.33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.007 2.03 89.5 0.903 0.339 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2FFU 2.007 20.027 1.73 163130 7888 97.1 0.1734 0.1711 0.1723 0.2189 0.2185 42.0352
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.443 f_angle_d 0.981 f_chiral_restr 0.059 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8846 Nucleic Acid Atoms Solvent Atoms 562 Heterogen Atoms 206
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing