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Structure of the N-terminal domain of BC2L-C lectin (1-131) in complex with a synthetic beta-N-fucoside ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WQ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 sodium citrate 1.2M
Crystal Properties Matthews coefficient Solvent content 1.8 31.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.931 α = 90 b = 42.931 β = 90 c = 94.882 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 2021-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.979 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 47.44 100 0.054 0.057 0.018 1 30.6 20.2 23283 11.2
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 1.34 100 0.48 0.505 0.158 0.959 6.7 20.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2wq4 1.32 37.179 23246 1163 99.996 0.105 0.1032 0.1121 0.1293 0.1393 14.674
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] 1.987 1.987 -3.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.07 r_dihedral_angle_3_deg 11.256 r_dihedral_angle_4_deg 10.751 r_dihedral_angle_1_deg 7.561 r_lrange_it 2.986 r_lrange_other 2.882 r_scangle_it 2.526 r_scangle_other 2.525 r_rigid_bond_restr 2.423 r_scbond_it 2.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.07 r_dihedral_angle_3_deg 11.256 r_dihedral_angle_4_deg 10.751 r_dihedral_angle_1_deg 7.561 r_lrange_it 2.986 r_lrange_other 2.882 r_scangle_it 2.526 r_scangle_other 2.525 r_rigid_bond_restr 2.423 r_scbond_it 2.09 r_scbond_other 2.088 r_mcangle_other 1.878 r_mcangle_it 1.876 r_angle_refined_deg 1.594 r_angle_other_deg 1.544 r_mcbond_it 1.47 r_mcbond_other 1.463 r_nbd_refined 0.206 r_symmetry_nbd_refined 0.206 r_nbd_other 0.198 r_symmetry_nbd_other 0.192 r_xyhbond_nbd_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.176 r_symmetry_nbtor_other 0.089 r_symmetry_xyhbond_nbd_other 0.087 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 987 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing