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Structure of the N terminal domain of Bc2L-C lectin (1-131) in complex with Globo H (H-type 3) antigen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TID
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 1.95 37.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.368 α = 90 b = 42.882 β = 96.007 c = 102.648 γ = 90
Symmetry Space Group C 1 2 1
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 2018-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97857 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 1.9 37.1 97.9 0.077 0.105 0.071 0.995 8.7 3.5 25081 17.8
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 1.9 1.94 97 0.363 0.486 0.32 0.861 2.9 3.5
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 6TID 1.9 37.1 25080 1552 97.546 0.169 0.1652 0.176 0.2265 0.2284 24.643
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] -1.21 0.157 -1.499 2.618
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.577 r_dihedral_angle_4_deg 13.144 r_dihedral_angle_3_deg 12.965 r_dihedral_angle_1_deg 7.986 r_lrange_it 6.575 r_lrange_other 6.483 r_scangle_it 4.77 r_scangle_other 4.77 r_mcangle_it 3.863 r_mcangle_other 3.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.577 r_dihedral_angle_4_deg 13.144 r_dihedral_angle_3_deg 12.965 r_dihedral_angle_1_deg 7.986 r_lrange_it 6.575 r_lrange_other 6.483 r_scangle_it 4.77 r_scangle_other 4.77 r_mcangle_it 3.863 r_mcangle_other 3.863 r_scbond_it 3.409 r_scbond_other 3.405 r_mcbond_it 2.944 r_mcbond_other 2.944 r_angle_refined_deg 1.998 r_angle_other_deg 1.491 r_symmetry_xyhbond_nbd_refined 0.248 r_nbd_refined 0.201 r_symmetry_nbd_other 0.192 r_xyhbond_nbd_refined 0.191 r_nbd_other 0.189 r_symmetry_nbd_refined 0.183 r_nbtor_refined 0.176 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.095 r_ncsr_local_group_2 0.073 r_ncsr_local_group_1 0.07 r_ncsr_local_group_3 0.07 r_symmetry_xyhbond_nbd_other 0.033 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2951 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 163
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing