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Structure of the N-terminal domain of BC2L-C lectin (1-131) in complex with a synthetic beta-fucosylamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TID
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 292 1.2M Tri sodium citrate ph 7.0
Crystal Properties Matthews coefficient Solvent content 1.8 31.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.008 α = 90 b = 43.008 β = 90 c = 94.217 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 EIGER X 16M 2022-09-10 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 1.55 37.25 99.1 0.064 0.076 0.04 0.0998 17.8 5.6 14192
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 1.55 1.58 99.7 0.447 0.54 0.297 0.888 3.5 4.6
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 1.55 37.246 14191 734 98.94 0.144 0.1424 0.1426 0.1687 0.1697 10.393
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] 0.147 0.074 0.147 -0.477
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.438 r_dihedral_angle_3_deg 12.328 r_dihedral_angle_1_deg 7.574 r_lrange_it 5.616 r_lrange_other 5.254 r_dihedral_angle_2_deg 4.09 r_scangle_it 3.697 r_scangle_other 3.694 r_scbond_it 2.667 r_scbond_other 2.665
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.438 r_dihedral_angle_3_deg 12.328 r_dihedral_angle_1_deg 7.574 r_lrange_it 5.616 r_lrange_other 5.254 r_dihedral_angle_2_deg 4.09 r_scangle_it 3.697 r_scangle_other 3.694 r_scbond_it 2.667 r_scbond_other 2.665 r_mcangle_other 2.286 r_mcangle_it 2.275 r_angle_refined_deg 1.821 r_mcbond_other 1.52 r_mcbond_it 1.516 r_angle_other_deg 0.644 r_nbd_refined 0.208 r_symmetry_nbd_other 0.198 r_symmetry_nbd_refined 0.193 r_nbtor_refined 0.184 r_nbd_other 0.178 r_symmetry_xyhbond_nbd_refined 0.164 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.103 r_symmetry_nbtor_other 0.091 r_chiral_restr_other 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 955 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing