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Amuc0121_S1_15 in complex with O6 sulfated Lewis A antigen (6'S-LeA)
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, SITTING DROP 293 Morpheus B1:
30 % Precipitant mix 1 (40% v/v PEG 500 MME; 20 % w/v PEG 20000)
0.1 M Buffer system 1 pH 6.5 (Imidazole; MES monohydrate acid)
0.09 M Halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide)
36 mgml Amuc0121_C78S ,Co-crystallised with 1 mM 6S-LeA and soaked with ~5 mM ~72h
Crystal Properties Matthews coefficient Solvent content 2.36 47.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.04 α = 90 b = 64.15 β = 104.88 c = 151.36 γ = 90
Symmetry Space Group P 1 21 1
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 16M 2025-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97625 Diamond I04
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 1.92 58.75 99.4 0.991 9.3 6.8 1313104
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 1.92 1.95 0.421
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.92 57.856 191914 9703 99.367 0.209 0.2076 0.2149 0.236 0.2412 39.568
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] 2.339 0.88 0.332 -2.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.214 r_dihedral_angle_3_deg 14.671 r_dihedral_angle_2_deg 9.55 r_lrange_it 6.859 r_lrange_other 6.859 r_dihedral_angle_1_deg 6.479 r_scangle_it 5.778 r_scangle_other 5.778 r_mcangle_it 4.115 r_mcangle_other 4.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.214 r_dihedral_angle_3_deg 14.671 r_dihedral_angle_2_deg 9.55 r_lrange_it 6.859 r_lrange_other 6.859 r_dihedral_angle_1_deg 6.479 r_scangle_it 5.778 r_scangle_other 5.778 r_mcangle_it 4.115 r_mcangle_other 4.115 r_scbond_it 3.886 r_scbond_other 3.885 r_mcbond_it 3.083 r_mcbond_other 3.083 r_dihedral_angle_other_2_deg 2.211 r_angle_refined_deg 1.558 r_angle_other_deg 0.538 r_symmetry_nbd_refined 0.333 r_nbd_other 0.242 r_nbd_refined 0.219 r_symmetry_nbd_other 0.201 r_symmetry_xyhbond_nbd_refined 0.201 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.134 r_metal_ion_refined 0.126 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.072 r_symmetry_xyhbond_nbd_other 0.071 r_ncsr_local_group_9 0.064 r_ncsr_local_group_2 0.063 r_ncsr_local_group_3 0.061 r_ncsr_local_group_10 0.061 r_ncsr_local_group_1 0.059 r_ncsr_local_group_6 0.059 r_ncsr_local_group_7 0.059 r_ncsr_local_group_5 0.057 r_ncsr_local_group_4 0.052 r_ncsr_local_group_8 0.052 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18886 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 213
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing