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N terminal domain of BC2L-C lectin (1-131) in complex with a beta-fucosylamide side-product
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 1 M sodium citrate pH 6.78
Crystal Properties Matthews coefficient Solvent content 1.8 31.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.936 α = 90 b = 42.936 β = 90 c = 94.555 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 2023-12-16 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 1.32 34.6 99.9 0.094 0.105 0.047 0.996 13.6 10.3 23087
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 0.49 0.553 0.248 0.927 4
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 1.322 29.244 23052 1129 99.883 0.118 0.116 0.1218 0.1552 0.1593 11.925
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] -0.448 -0.224 -0.448 1.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.216 r_lrange_it 11.328 r_lrange_other 9.788 r_dihedral_angle_3_deg 9.592 r_scangle_it 7.279 r_scangle_other 7.274 r_dihedral_angle_1_deg 6.993 r_scbond_it 5.299 r_scbond_other 5.299 r_rigid_bond_restr 5.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.216 r_lrange_it 11.328 r_lrange_other 9.788 r_dihedral_angle_3_deg 9.592 r_scangle_it 7.279 r_scangle_other 7.274 r_dihedral_angle_1_deg 6.993 r_scbond_it 5.299 r_scbond_other 5.299 r_rigid_bond_restr 5.229 r_mcangle_other 4.899 r_mcangle_it 4.89 r_mcbond_it 3.618 r_mcbond_other 3.575 r_dihedral_angle_2_deg 2.213 r_angle_refined_deg 1.837 r_angle_other_deg 0.606 r_symmetry_nbd_refined 0.26 r_nbd_other 0.214 r_symmetry_xyhbond_nbd_refined 0.208 r_symmetry_nbd_other 0.206 r_nbd_refined 0.191 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.184 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 967 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing