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X-ray crystal structure of Toxoplasma gondii GalNAc-T3 at pH 7.3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8UHV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 293 Crystals were grown in buffer containing 0.1 M CHES pH 9.5 and 14-20% PEG 8000 (w/v) and soaked in cryo buffer containing 20% glycerol and HEPES pH 7.3.
Crystal Properties Matthews coefficient Solvent content 2.61 52.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.43 α = 90 b = 65.713 β = 90 c = 166.314 γ = 90
Symmetry Space Group P 2 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 CCD RAYONIX MX300-HS 2022-10-28 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) R Merge 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 2.9 30 98 0.178 0.193 0.074 0.986 11.8 6.7 15343 63.88
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.95 96.5 1.204 1.363 0.618 0.297 1.08 4.5
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 2.91 29.68 1.36 15289 1541 97.58 0.1892 0.1848 0.1848 0.227 0.2268 60.23
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 15.9184 f_angle_d 0.6135 f_chiral_restr 0.0413 f_plane_restr 0.0096 f_bond_d 0.0032
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4163 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 63
Software Software Software Name Purpose HKL-2000 data collection PHENIX refinement HKL-2000 data reduction MOLREP phasing Aimless data scaling