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Structure of the N-terminal domain of BC2L-C lectin (1-131) in complex with a synthetic beta-C-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 1.87 34.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.954 α = 90 b = 43.954 β = 90 c = 94.138 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 9M 2020-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980 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 1.79 47.07 99.7 0.039 0.041 0.013 1 49.1 20.2 9696 20.9
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 1.79 1.83 95.4 0.228 0.241 0.077 0.99 11.1 17.2
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 1.793 38.065 9670 454 99.66 0.142 0.1396 0.1506 0.1942 0.2018 25.797
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] -5.611 -5.611 11.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.58 r_dihedral_angle_4_deg 19.337 r_dihedral_angle_3_deg 11.879 r_dihedral_angle_1_deg 8.145 r_lrange_it 6.578 r_lrange_other 6.564 r_scangle_it 5.156 r_scangle_other 5.152 r_mcangle_it 4.023 r_mcangle_other 4.021
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.58 r_dihedral_angle_4_deg 19.337 r_dihedral_angle_3_deg 11.879 r_dihedral_angle_1_deg 8.145 r_lrange_it 6.578 r_lrange_other 6.564 r_scangle_it 5.156 r_scangle_other 5.152 r_mcangle_it 4.023 r_mcangle_other 4.021 r_scbond_it 3.64 r_scbond_other 3.638 r_mcbond_it 2.983 r_mcbond_other 2.972 r_angle_refined_deg 1.825 r_angle_other_deg 1.53 r_symmetry_xyhbond_nbd_refined 0.242 r_symmetry_nbd_other 0.202 r_nbd_refined 0.196 r_nbd_other 0.184 r_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.173 r_symmetry_nbd_refined 0.151 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.089 r_bond_refined_d 0.016 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 978 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing