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Pasteurella multocida alpha2,3/2,6 sialyltransferase D141N bound to CMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IIB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 14 mg/mL PMSTD141N protein in 20 mM Tris pH 7.5
mother liquor: 23% PEG 3350
100 mM HEPES, pH 6.0
100 mM NaCl
0.4% Triton X-100
5 mM CMP
Drops were 1:1 protein and mother liquor.
Crystal Properties Matthews coefficient Solvent content 2.39 48.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.598 α = 90 b = 66.401 β = 90 c = 96.383 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 9M 2023-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12704 APS 21-ID-D
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 1.84 50 99.9 0.999 47.83 12.4 38024 26.68
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 1.84 1.88 0.961
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 1.84 31.89 1.36 37943 1867 99.43 0.2169 0.215 0.2149 0.2535 0.2528 35.03
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 7.0251 f_angle_d 1.0233 f_chiral_restr 0.0559 f_bond_d 0.0082 f_plane_restr 0.0062
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3126 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 46
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing