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Crystal structure of the Mucin-type O-glycosyltransferase PGANT5A-4M (A430T, L434N, A437N, S456Y)
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, HANGING DROP 7.2 293.15 PEG 3350, HEPES, magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.27 45.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.113 α = 81.7 b = 89.17 β = 81.73 c = 129.525 γ = 71.06
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 EIGER2 S 9M 2024-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 1 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) 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 3.08 29.77 94.7 0.12 0.138 0.17 0.12 0.962 6.5 1 44420
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.08 3.15 96.7 0.965 1.213 1.365 0.965 0.224 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 3.08 29.77 1.96 44019 2203 93.91 0.2037 0.201 0.202 0.2553 0.2563
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 10.927 f_angle_d 0.518 f_chiral_restr 0.052 f_plane_restr 0.006 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16957 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 343
Software Software Software Name Purpose PHENIX refinement Aimless data scaling HKL-2000 data reduction MOLREP phasing PDB_EXTRACT data extraction