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N terminal domain of BC2L-C lectin in complex with N-(beta-L-Fucopyranosyl)-biphenyl-3-carboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WQ4 trimer experimental model PDB 6TID monomer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 17% Peg10K, 100 mM sodium acetate and 100 mM Bis-Tris pH 5.5 cryo in 7.6% Peg10K, 22.5% Peg Smear Low, 45 mM sodium acetate and Bis Tris pH 5.5 and 3 mM PMA127
Crystal Properties Matthews coefficient Solvent content 3.4 63.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.506 α = 90 b = 169.506 β = 90 c = 344.036 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 2024-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.97856 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 2.55 48.932 100 0.091 0.1 0.041 0.999 18.6 11.6 62109
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 2.55 2.62 0.916 1 0.403 0.831 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.55 48.932 62106 3061 99.969 0.181 0.1791 0.2219 0.2007 51.209
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] 0.809 0.404 0.809 -2.623
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.526 r_dihedral_angle_2_deg 15.217 r_dihedral_angle_6_deg 14.188 r_lrange_it 10.179 r_lrange_other 10.17 r_scangle_it 8.692 r_scangle_other 8.691 r_dihedral_angle_1_deg 7.343 r_mcangle_other 7.209 r_mcangle_it 7.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.526 r_dihedral_angle_2_deg 15.217 r_dihedral_angle_6_deg 14.188 r_lrange_it 10.179 r_lrange_other 10.17 r_scangle_it 8.692 r_scangle_other 8.691 r_dihedral_angle_1_deg 7.343 r_mcangle_other 7.209 r_mcangle_it 7.208 r_scbond_it 6.816 r_scbond_other 6.816 r_mcbond_it 5.635 r_mcbond_other 5.625 r_angle_refined_deg 1.889 r_angle_other_deg 0.599 r_symmetry_xyhbond_nbd_refined 0.286 r_symmetry_nbd_other 0.215 r_nbd_refined 0.199 r_nbtor_refined 0.188 r_nbd_other 0.165 r_xyhbond_nbd_refined 0.15 r_symmetry_nbd_refined 0.146 r_chiral_restr_other 0.105 r_symmetry_nbtor_other 0.093 r_chiral_restr 0.087 r_ncsr_local_group_14 0.08 r_ncsr_local_group_41 0.077 r_ncsr_local_group_23 0.075 r_ncsr_local_group_26 0.075 r_ncsr_local_group_20 0.074 r_ncsr_local_group_38 0.074 r_ncsr_local_group_36 0.072 r_ncsr_local_group_13 0.071 r_ncsr_local_group_29 0.071 r_ncsr_local_group_42 0.071 r_ncsr_local_group_3 0.07 r_ncsr_local_group_10 0.07 r_ncsr_local_group_6 0.069 r_ncsr_local_group_11 0.069 r_ncsr_local_group_31 0.069 r_ncsr_local_group_43 0.068 r_ncsr_local_group_5 0.067 r_ncsr_local_group_21 0.067 r_ncsr_local_group_24 0.067 r_ncsr_local_group_27 0.067 r_ncsr_local_group_2 0.066 r_ncsr_local_group_34 0.066 r_ncsr_local_group_1 0.065 r_ncsr_local_group_12 0.065 r_ncsr_local_group_22 0.064 r_ncsr_local_group_28 0.063 r_ncsr_local_group_30 0.063 r_ncsr_local_group_8 0.062 r_ncsr_local_group_4 0.061 r_ncsr_local_group_18 0.061 r_ncsr_local_group_35 0.061 r_ncsr_local_group_15 0.06 r_ncsr_local_group_16 0.06 r_ncsr_local_group_37 0.059 r_ncsr_local_group_25 0.057 r_ncsr_local_group_32 0.057 r_ncsr_local_group_33 0.057 r_ncsr_local_group_39 0.057 r_ncsr_local_group_40 0.057 r_ncsr_local_group_45 0.057 r_ncsr_local_group_9 0.056 r_ncsr_local_group_19 0.056 r_ncsr_local_group_44 0.054 r_ncsr_local_group_7 0.052 r_ncsr_local_group_17 0.05 r_symmetry_xyhbond_nbd_other 0.045 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9591 Nucleic Acid Atoms Solvent Atoms 367 Heterogen Atoms 351
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing