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N terminal domain of BC2L-C lectin (1-131) with covalent beta-fucosylamide ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BRO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 0.9 M sodium citrate pH 6.78
Crystal Properties Matthews coefficient Solvent content 3.64 66.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.336 α = 90 b = 113.336 β = 90 c = 63.263 γ = 90
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 2024-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.97856 SOLEIL PROXIMA 2
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 1.95 39.56 100 0.093 0.106 0.05 0.999 12.3 8.5 29351
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 1.95 2 0.813 0.926 0.438 0.892 2.2
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 1.95 39.556 29340 1458 99.983 0.182 0.1787 0.1894 0.233 0.2364 35.411
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] -25.115 -25.115 50.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.294 r_dihedral_angle_3_deg 12.759 r_lrange_other 8.566 r_lrange_it 8.557 r_dihedral_angle_1_deg 7.622 r_scangle_it 7.28 r_scangle_other 7.278 r_mcangle_it 5.976 r_mcangle_other 5.976 r_scbond_it 5.714
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.294 r_dihedral_angle_3_deg 12.759 r_lrange_other 8.566 r_lrange_it 8.557 r_dihedral_angle_1_deg 7.622 r_scangle_it 7.28 r_scangle_other 7.278 r_mcangle_it 5.976 r_mcangle_other 5.976 r_scbond_it 5.714 r_scbond_other 5.714 r_mcbond_it 5.166 r_mcbond_other 5.157 r_dihedral_angle_2_deg 3.97 r_angle_refined_deg 1.974 r_angle_other_deg 0.619 r_symmetry_nbd_refined 0.245 r_nbd_other 0.202 r_symmetry_nbd_other 0.2 r_nbd_refined 0.198 r_symmetry_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.141 r_ncsr_local_group_2 0.107 r_ncsr_local_group_3 0.101 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.094 r_ncsr_local_group_1 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2882 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing