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Structure of the N terminal domain of Bc2L-C lectin (1-131) in complex with Globo H (H-type 3) and CAS No 912569-62-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TIG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 5.5 mg/ml of protein, 1.2 M sodium citrate, 10 mM ligand at 292 K temperature and cryoprotected with 2.5 M sodium malonate
Crystal Properties Matthews coefficient Solvent content 1.95 37.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.459 α = 90 b = 42.912 β = 96.1 c = 103.345 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 2020-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9786 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 37.13 98.8 0.134 0.146 0.055 0.994 10.2 6.9 25522
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 98.1 0.531 0.573 0.214 0.898 7.1
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6tig 1.9 37.13 24288 1224 98.43 0.1836 0.1809 0.2382 0.2411 RANDOM 20.848
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] -0.95 0.12 -1.31 2.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.078 r_dihedral_angle_3_deg 14.246 r_dihedral_angle_4_deg 10.999 r_dihedral_angle_1_deg 7.103 r_angle_refined_deg 1.84 r_angle_other_deg 1.496 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.078 r_dihedral_angle_3_deg 14.246 r_dihedral_angle_4_deg 10.999 r_dihedral_angle_1_deg 7.103 r_angle_refined_deg 1.84 r_angle_other_deg 1.496 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2881 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 206
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing