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Galectin-3 in Complex with Methyl 2'-fluoro-N-acetyllactosaminide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ODY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 150 mM KBr, 20% PEG MME 2000
Crystal Properties Matthews coefficient Solvent content 2.16 43.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.091 α = 90 b = 58.046 β = 90 c = 63.664 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 2M 2021-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 0.989 42.93 99.6 0.062 0.999 15.4 6.4 147991 12.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.989 1.05 97.7 1.161 0.603 1.39 5.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 0.989 42.93 77282 2319 99.683 0.134 0.1334 0.1362 0.158 0.1603 11.721
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] 1.433 -0.946 -0.486
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.928 r_lrange_it 13.683 r_dihedral_angle_3_deg 11.571 r_lrange_other 10.783 r_dihedral_angle_2_deg 8.032 r_dihedral_angle_1_deg 7.634 r_scangle_it 5.66 r_scangle_other 5.657 r_scbond_it 4.1 r_scbond_other 4.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.928 r_lrange_it 13.683 r_dihedral_angle_3_deg 11.571 r_lrange_other 10.783 r_dihedral_angle_2_deg 8.032 r_dihedral_angle_1_deg 7.634 r_scangle_it 5.66 r_scangle_other 5.657 r_scbond_it 4.1 r_scbond_other 4.097 r_mcangle_other 3.928 r_mcangle_it 3.923 r_rigid_bond_restr 3.922 r_mcbond_it 2.828 r_mcbond_other 2.802 r_angle_refined_deg 2.029 r_angle_other_deg 0.749 r_nbd_refined 0.225 r_symmetry_nbd_other 0.211 r_nbd_other 0.209 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.138 r_symmetry_nbd_refined 0.138 r_symmetry_xyhbond_nbd_refined 0.138 r_chiral_restr 0.124 r_symmetry_xyhbond_nbd_other 0.107 r_symmetry_nbtor_other 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_chiral_restr_other 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1108 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing