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Structure of the N-terminal domain of CMA in complex with N-acetyllactosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold A0A1S4E5V9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 10% Peg Smear Medium, 0.1 M Mes pH 6.5, and 5 mM of CaCl2, MgCl2, CsCl2, CdCl2, NiCl2 and Zinc acetate
transfered in 30% Peg Smear Medium 5mM CdCl2 for cryoprotection
Crystal Properties Matthews coefficient Solvent content 2.29 46.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.696 α = 90 b = 36.782 β = 99.237 c = 94.786 γ = 90
Symmetry Space Group I 1 2 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 EIGER X 16M 2023-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97856 SOLEIL PROXIMA 1
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 1.317 46.78 99.8 0.055 0.059 0.022 0.999 25.2 13.5 29695
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 1.32 1.34 0.369 0.4 0.153 0.969 5.7
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 1.317 46.778 29694 1503 99.798 0.146 0.1435 0.1531 0.1858 0.194 13.471
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] -0.245 -0.068 0.761 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.075 r_dihedral_angle_3_deg 14 r_lrange_it 11.386 r_lrange_other 10.265 r_scangle_it 8.283 r_scangle_other 8.277 r_scbond_it 6.411 r_scbond_other 6.406 r_dihedral_angle_1_deg 6.145 r_mcangle_it 5.852
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.075 r_dihedral_angle_3_deg 14 r_lrange_it 11.386 r_lrange_other 10.265 r_scangle_it 8.283 r_scangle_other 8.277 r_scbond_it 6.411 r_scbond_other 6.406 r_dihedral_angle_1_deg 6.145 r_mcangle_it 5.852 r_mcangle_other 5.852 r_rigid_bond_restr 5.716 r_mcbond_it 4.445 r_mcbond_other 4.444 r_angle_refined_deg 1.721 r_dihedral_angle_2_deg 1.385 r_angle_other_deg 0.616 r_symmetry_metal_ion_refined 0.287 r_symmetry_nbd_refined 0.229 r_symmetry_nbd_other 0.214 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.193 r_nbd_other 0.188 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.142 r_metal_ion_refined 0.12 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 953 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing