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Structure of the N-terminal domain of BC2L-C lectin (1-131) in complex with Lewis y antigen
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 1.96 37.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.887 α = 90 b = 42.887 β = 90 c = 310.001 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 1.92 36.88 100 0.073 0.077 0.026 0.999 23.8 15.6 8958 16.9
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 1.92 1.97 100 0.399 0.424 0.143 0.982 7.3
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 1.92 36.88 8957 429 99.922 0.154 0.152 0.1637 0.1934 0.2023 27.301
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] 0.066 0.033 0.066 -0.214
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.155 r_dihedral_angle_3_deg 12.893 r_dihedral_angle_4_deg 12.001 r_lrange_it 8.702 r_lrange_other 8.574 r_dihedral_angle_1_deg 7.305 r_scangle_it 6.398 r_scangle_other 6.394 r_mcangle_it 4.528 r_mcangle_other 4.525
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.155 r_dihedral_angle_3_deg 12.893 r_dihedral_angle_4_deg 12.001 r_lrange_it 8.702 r_lrange_other 8.574 r_dihedral_angle_1_deg 7.305 r_scangle_it 6.398 r_scangle_other 6.394 r_mcangle_it 4.528 r_mcangle_other 4.525 r_scbond_it 4.389 r_scbond_other 4.388 r_mcbond_it 3.323 r_mcbond_other 3.321 r_angle_refined_deg 1.973 r_angle_other_deg 1.549 r_chiral_restr 0.431 r_symmetry_xyhbond_nbd_refined 0.23 r_xyhbond_nbd_refined 0.213 r_nbd_other 0.204 r_nbd_refined 0.199 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.177 r_symmetry_nbd_refined 0.147 r_symmetry_nbtor_other 0.093 r_symmetry_xyhbond_nbd_other 0.076 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_xyhbond_nbd_other 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 982 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing