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Understanding the singular conformational landscape of the Tn antigens: Sulfur-for- oxygen substitution in the glycosidic linkage provides new insights into molecular recognition by an antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A2I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 20% PEG 3350, 0.2 M disodium hydrogen phosphate
Crystal Properties Matthews coefficient Solvent content 2.09 41.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.403 α = 90 b = 68.648 β = 90 c = 90.917 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 PILATUS3 S 6M 2016-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.7 20 99.9 0.035 0.999 13 6.3 25141
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 1.7 1.79 100 0.317 0.867 2.4 6.4
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 5A2I 1.7 20 24415 675 99.85 0.17705 0.17606 0.1865 0.21062 0.2206 RANDOM 24.071
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] 0.39 1.31 -1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.687 r_dihedral_angle_4_deg 23.35 r_dihedral_angle_3_deg 13.097 r_dihedral_angle_1_deg 6.057 r_long_range_B_other 4.976 r_long_range_B_refined 4.975 r_scangle_other 2.928 r_mcangle_it 2.002 r_mcangle_other 2.001 r_scbond_it 1.819
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.687 r_dihedral_angle_4_deg 23.35 r_dihedral_angle_3_deg 13.097 r_dihedral_angle_1_deg 6.057 r_long_range_B_other 4.976 r_long_range_B_refined 4.975 r_scangle_other 2.928 r_mcangle_it 2.002 r_mcangle_other 2.001 r_scbond_it 1.819 r_scbond_other 1.815 r_angle_refined_deg 1.54 r_angle_other_deg 1.45 r_mcbond_it 1.269 r_mcbond_other 1.269 r_chiral_restr 0.122 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.001 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 1769 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing