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Crystal structure of the C. elegans POFUT2 (CePoFUT2) triple mutant (R298K-R299K-A418C) in complex with the Rattus norvegicus TSR4 single mutant (E10C) from F-spondin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FOE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 BIS-Tris
calcium chloride dihydrate
MPD
ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.69 54.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.848 α = 90 b = 156.848 β = 90 c = 80.451 γ = 120
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 S 6M 2019-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9793 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 2.13 20 99.6 0.032 0.998 10.6 8.5 62973
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 2.13 2.24 98.1 0.765 0.491 1.1 8.1
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 5FOE 2.13 19.9 60376 2439 99.33 0.19531 0.19351 0.2014 0.24037 0.2424 RANDOM 61.322
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] 0.05 0.02 0.05 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.376 r_dihedral_angle_2_deg 10.939 r_long_range_B_refined 10.506 r_long_range_B_other 10.506 r_scangle_other 8.314 r_dihedral_angle_1_deg 7.277 r_mcangle_other 6.681 r_mcangle_it 6.68 r_scbond_it 6.074 r_scbond_other 5.953
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.376 r_dihedral_angle_2_deg 10.939 r_long_range_B_refined 10.506 r_long_range_B_other 10.506 r_scangle_other 8.314 r_dihedral_angle_1_deg 7.277 r_mcangle_other 6.681 r_mcangle_it 6.68 r_scbond_it 6.074 r_scbond_other 5.953 r_mcbond_it 4.967 r_mcbond_other 4.965 r_angle_refined_deg 1.389 r_angle_other_deg 0.482 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 6931 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing